Re: [Freesurfer] [FreeSurfer] WM Parcellation

[Douglas N Greve]

You can regenerate a wmparc that does not have the unsegmented wm with 
something like

cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown 
--volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o mri/wmparc2.mgz

Then create your lobes from that


On 01/27/2016 05:47 PM, VA Research wrote:
> Hello FS experts,
>
> Does anyone have some form of step-by-step instructions on how to do 
> this ?
>
> Thanks so much
>
> Joseph
> Brainiac . wrote:
> >/Hi All, />//>/I need to classify WM into different lobes (temporal, 
> >parietal, />/frontal, occipital). I tried to do the lobe mapping using 
> >/>/parcellations from wmparc.mgz. 
> >/>/http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation />//>/My 
> >problem is the "unsegmented white matter" in wmparc.mgz. My />/understanding 
> >is that these unsegmented areas are classified so />/because they are beyond 
> >5mm from any pre-classified cortex area. />//>/My questions: />/(1) So in 
> >order to classify "unsegmented WM" into lobes, do I need to />/take each 
> >voxel in the unsegmented WM region and then assign it to the />/closest 
> >cortex area to classify it into respective parcellations. Then />/re-group 
> >into lobes. Is this correct? /
> >//>/(2) Are there any tailor made function or any other easier way to do 
> >/>/this? Is there any easier way to segment WM into lobes directly that I 
> >/>/have missed? />//>/Thanks, />/Brain/
>
> You can do this in a couple of steps. First, you'll need to create a
> lobe annotation. You can do this in 3 ways:
> 1. mri_annotation2label --lobesStrict
>2. mri_annotation2label --lobes
>3. Custom: break up annotation and recombine:
>a. mri_annotation to create separate label files
>b. mri_mergelabels to create single label files for each lobe label
>c. mris_label2annot to create the lobe annotation
>
> Next, create the WM segmentation with mri_aparc2aseg, specifying your
> new lobe annot and adding --labelwm. You can control the distance  with
> --wmparc-dmax
>
> doug
>
>
> ___
> 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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[Freesurfer] R: Ref FAST and results visualization issue

[stdp82]

Briefly, is possible to map the fictional connectivity between a right seed and 
left cortex?
Stefano




Messaggio originale

Da: std...@virgilio.it

Data: 27-gen-2016 18.57

A: 

Ogg: [Freesurfer] Ref FAST and results visualization issue



Hi list, 
I have two requests please.
A- I need to have a reference for FS-FAST (seed based analysis on rs data)
B- I have difficulties for results visualization. How can I do to visualize the 
the cortical areas which are functionally connected with the controlateral 
seed? 
For example, my seed are right and left amygdala.To visualize RIGHT amygdala - 
RIGHT cortex connectivity I'm doing:
cd my-group/fc.ramgseed.surf.lh/R_Amygdala
tksurfer fsaverage rh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz

and all is fine.
To visualize RIGHT amygdala - LEFT cortex connectivity I'm doing:

tksurfer fsaverage lh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz

but the image is so confused. It seem to be the translated image which I have 
projected in the right semi.

Thanks

Stefano



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Re: [Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

[John Plass]

Hi Doug,
The geometry of the input is correct in both freeview and tkmedit, and the
outlines of the white and pial surfaces align well with with volume in
freeview. Looking at the headers, I'm wondering if my initial transform of
the image into the proper coordinates might be the problem. The DICOM
wasn't oriented correctly at first, so I converted to nifti, and ran
"mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz
mprage.mgz", which produced a conformed image with the correct orientation
in freeview. Is there a chance that a problem here could produce the
problems later down the pipeline? For example, I see now that
mprage.nii.gz's header correctly lists the primary slice direction as
axial, whereas the reoriented mprage.mgz incorrectly lists it as coronal.
Also, orientation was originally listed as RAS, but changed to LIA after
conversion. Is there a chance that this is affecting the later surface
registration?

Thanks so much for any help you can provide. I've attached mri_info output
for the nifti and mgz files below.

Best regards,
John

mri_info mprage.nii.gz
Volume information for mprage.nii.gz
  type: nii
dimensions: 199 x 152 x 183
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 199.000
   dof: 0
xstart: -99.5, xend: 99.5
ystart: -76.0, yend: 76.0
zstart: -91.5, zend: 91.5
TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =   0.7324, y_r =   0.0361, z_r =   0.6799, c_r =
1.7748
  : x_a =  -0.0157, y_a =   0.9992, z_a =  -0.0361, c_a =
25.8853
  : x_s =  -0.6807, y_s =   0.0157, z_s =   0.7324, c_s =
-8.5852
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
0.7324   0.0361   0.6799  -136.0543
   -0.0157   0.9992  -0.0361   -45.1875
   -0.6807   0.0157   0.7324-9.0720
0.   0.   0. 1.

voxel-to-ras determinant 0.97

ras to voxel transform:
0.7324  -0.0157  -0.680792.7637
0.0361   0.9992   0.015750.2057
0.6799  -0.0361   0.732497.5155
0.   0.   0. 1.

__

mri_info mprage.mgz
Volume information for mprage.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
1.7748
  : x_a =   0., y_a =   0., z_a =   1., c_a =
25.8853
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
-8.5852

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   129.7748
0.   0.   1.  -102.1147
0.  -1.   0.   119.4148
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.   129.7748
   -0.  -0.  -1.   119.4148
   -0.   1.  -0.   102.1147
0.   0.   0. 1.




---
John Plass
Ph.D. Candidate
Visual Perception, Neuroscience, and Cognition Lab
Northwestern University

On Wed, Jan 27, 2016 at 1:43 PM, Douglas N Greve 
wrote:

> I don't know how that could have happened.  Is the geometry of the
> exvivo input oriented correctly? Ie, if you load the orig.mgz into
> freeview or tkmedit, is sag actually sagital, etc?
>
> On 01/26/2016 06:08 PM, John Plass wrote:
> > Hi Bruce,
> > Thanks for your reply. The orientation is correct in freeview,
> > although, digging further, I see that that it is misoriented when I
> > view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal
> > --surf orig, and the orig volume is shown oriented correctly, but the
> > orig surface appears to have some of the dimensions swapped. Any idea
> > why this might be?
> >
> > Thanks for your help!
> >
> > John
> >
> > On Tuesday, January 26, 2016, Bruce Fischl  > > wrote:
> >
> > Hi John
> >
> > does it come up in the correct orientation in freeview? If you didn't
> > scan it in the orientation that a person would have been lying in the
> > scanner, you will need to reorient the data so that we know what e.g.
> > anterior is
> >
> > cheers
> > Bruce
> >
> > On Tue, 26 Jan 2016, John Plass wrote:
> >
> > > Hello,
> > > I've been 

Re: [Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

[Douglas N Greve]

I think if they look ok in freeview and tkmedit, then they are probably 
ok. Can you tar up and upload the data set to me?

https://gate.nmr.mgh.harvard.edu/filedrop2


On 01/27/2016 06:05 PM, John Plass wrote:
> Hi Doug,
> The geometry of the input is correct in both freeview and tkmedit, and 
> the outlines of the white and pial surfaces align well with with 
> volume in freeview. Looking at the headers, I'm wondering if my 
> initial transform of the image into the proper coordinates might be 
> the problem. The DICOM wasn't oriented correctly at first, so I 
> converted to nifti, and ran "mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 
> -ikd 1 0 0 mprage.nii.gz  mprage.mgz", which produced a conformed 
> image with the correct orientation in freeview. Is there a chance that 
> a problem here could produce the problems later down the pipeline? For 
> example, I see now that mprage.nii.gz's header correctly lists the 
> primary slice direction as axial, whereas the reoriented mprage.mgz 
> incorrectly lists it as coronal. Also, orientation was originally 
> listed as RAS, but changed to LIA after conversion. Is there a chance 
> that this is affecting the later surface registration?
>
> Thanks so much for any help you can provide. I've attached mri_info 
> output for the nifti and mgz files below.
>
> Best regards,
> John
>
> mri_info mprage.nii.gz
> Volume information for mprage.nii.gz
>   type: nii
> dimensions: 199 x 152 x 183
>voxel sizes: 1., 1., 1.
>   type: FLOAT (3)
>fov: 199.000
>dof: 0
> xstart: -99.5, xend: 99.5
> ystart: -76.0, yend: 76.0
> zstart: -91.5, zend: 91.5
> TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
> 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =   0.7324, y_r =   0.0361, z_r =   0.6799, c_r 
> = 1.7748
>   : x_a =  -0.0157, y_a =   0.9992, z_a =  -0.0361, c_a 
> =25.8853
>   : x_s =  -0.6807, y_s =   0.0157, z_s =   0.7324, c_s 
> =-8.5852
> Orientation   : RAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
> 0.7324   0.0361   0.6799  -136.0543
>-0.0157   0.9992  -0.0361   -45.1875
>-0.6807   0.0157   0.7324-9.0720
> 0.   0.   0. 1.
>
> voxel-to-ras determinant 0.97
>
> ras to voxel transform:
> 0.7324  -0.0157  -0.680792.7637
> 0.0361   0.9992   0.015750.2057
> 0.6799  -0.0361   0.732497.5155
> 0.   0.   0. 1.
>
> __
>
> mri_info mprage.mgz
> Volume information for mprage.mgz
>   type: MGH
> dimensions: 256 x 256 x 256
>voxel sizes: 1., 1., 1.
>   type: UCHAR (0)
>fov: 256.000
>dof: 0
> xstart: -128.0, xend: 128.0
> ystart: -128.0, yend: 128.0
> zstart: -128.0, zend: 128.0
> TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
> 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r 
> = 1.7748
>   : x_a =   0., y_a =   0., z_a =   1., c_a 
> =25.8853
>   : x_s =   0., y_s =  -1., z_s =   0., c_s 
> =-8.5852
>
> talairach xfm :
> Orientation   : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>-1.   0.   0.   129.7748
> 0.   0.   1.  -102.1147
> 0.  -1.   0.   119.4148
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>-1.   0.   0.   129.7748
>-0.  -0.  -1.   119.4148
>-0.   1.  -0.   102.1147
> 0.   0.   0. 1.
>
>
>
>
> ---
> John Plass
> Ph.D. Candidate
> Visual Perception, Neuroscience, and Cognition Lab
> Northwestern University
>
> On Wed, Jan 27, 2016 at 1:43 PM, Douglas N Greve 
> > wrote:
>
> I don't know how that could have happened.  Is the geometry of the
> exvivo input oriented correctly? Ie, if you load the orig.mgz into
> freeview or tkmedit, is sag actually sagital, etc?
>
> On 01/26/2016 06:08 PM, John Plass wrote:
> > Hi Bruce,
> > Thanks for your reply. The orientation is correct in freeview,
> > although, digging further, I see that that it is misoriented when I
> > view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal
> > --surf orig, and the orig volume is shown oriented correctly,
> but the
> > orig surface appears to have some of the dimensions swapped. Any
> idea
> > why this might be?
> >
> > 

Re: [Freesurfer] [FreeSurfer] WM Parcellation

[Douglas N Greve]

First you'll have to decide on which wm parcellations will go into which 
lobe. When you have that, then you can use mri_binarize with the 
--replace option to change the index of a given segmentation to that of 
the lobe

On 01/27/2016 07:00 PM, VA Research wrote:
> thank you for that,
>
> but i'm confused on how to do the rest as well .
>
> I now have the wmparc2 with unsegmented areas,
>
> how can we create the lobar regions and use those to parcelate the WM into
>
> lobar regions?
>
> On Wed, Jan 27, 2016 at 2:57 PM, Douglas N Greve 
> > wrote:
>
> You can regenerate a wmparc that does not have the unsegmented wm with
> something like
>
> cd $SUBJECTS_DIR/subject
> mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
> --volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o
> mri/wmparc2.mgz
>
> Then create your lobes from that
>
>
> On 01/27/2016 05:47 PM, VA Research wrote:
> > Hello FS experts,
> >
> > Does anyone have some form of step-by-step instructions on how to do
> > this ?
> >
> > Thanks so much
> >
> > Joseph
> > Brainiac . wrote:
> > >/Hi All, />//>/I need to classify WM into different lobes
> (temporal, parietal, />/frontal, occipital). I tried to do the
> lobe mapping using />/parcellations from wmparc.mgz.
> />/http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
> />//>/My problem is the "unsegmented white matter" in wmparc.mgz.
> My />/understanding is that these unsegmented areas are classified
> so />/because they are beyond 5mm from any pre-classified cortex
> area. />//>/My questions: />/(1) So in order to classify
> "unsegmented WM" into lobes, do I need to />/take each voxel in
> the unsegmented WM region and then assign it to the />/closest
> cortex area to classify it into respective parcellations. Then
> />/re-group into lobes. Is this correct? /
> > >//>/(2) Are there any tailor made function or any other easier
> way to do />/this? Is there any easier way to segment WM into
> lobes directly that I />/have missed? />//>/Thanks, />/Brain/
> >
> > You can do this in a couple of steps. First, you'll need to create a
> > lobe annotation. You can do this in 3 ways:
> > 1. mri_annotation2label --lobesStrict
> >2. mri_annotation2label --lobes
> >3. Custom: break up annotation and recombine:
> >a. mri_annotation to create separate label files
> >b. mri_mergelabels to create single label files for each
> lobe label
> >c. mris_label2annot to create the lobe annotation
> >
> > Next, create the WM segmentation with mri_aparc2aseg, specifying
> your
> > new lobe annot and adding --labelwm. You can control the
> distance  with
> > --wmparc-dmax
> >
> > doug
> >
> >
> > ___
> > 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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: 

[Freesurfer] [FreeSurfer] WM Parcellation

[VA Research]

Hello FS experts,

Does anyone have some form of step-by-step instructions on how to do this ?

Thanks so much

Joseph

Brainiac . wrote:
>* Hi All,
*>>* I need to classify WM into different lobes (temporal, parietal,
*>* frontal, occipital). I tried to do the lobe mapping using
*>* parcellations from wmparc.mgz.
*>* http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

*>  >* My problem is the "unsegmented white matter" in wmparc.mgz. My
*>* understanding is that these unsegmented areas are classified so
*>* because they are beyond 5mm from any pre-classified cortex area.
*>>* My questions:
*>* (1) So in order to classify "unsegmented WM" into lobes, do I need to
*>* take each voxel in the unsegmented WM region and then assign it to the
*>* closest cortex area to classify it into respective parcellations. Then
*>* re-group into lobes. Is this correct?
*
>>* (2) Are there any tailor made function or any other easier way to do
*>* this? Is there any easier way to segment WM into lobes directly that I
*>* have missed?
*>>* Thanks,
*>* Brain*


You can do this in a couple of steps. First, you'll need to create a
lobe annotation. You can do this in 3 ways:
   1. mri_annotation2label --lobesStrict
  2. mri_annotation2label --lobes
  3. Custom: break up annotation and recombine:
  a. mri_annotation to create separate label files
  b. mri_mergelabels to create single label files for each lobe label
  c. mris_label2annot to create the lobe annotation

Next, create the WM segmentation with mri_aparc2aseg, specifying your
new lobe annot and adding --labelwm. You can control the distance  with
--wmparc-dmax

doug
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[Freesurfer] mail option to email custom status of job completion

[Sneha Pandya]

Dear experts,


I usually setup batch jobs for my studies and use '-mail' option that emails me 
completion of recon-all with or without errors. Is there a way or any other 
option that I can use alongside '-mail' to give me custom status message than 
the usual one which says "recon-all -s XYZ finished without error at ...". For 
example if I have set up to run subjects XYZ for only autorecon2 stage, I would 
like it to send me an email message saying "recon-all autorecon-2 finished 
without error" or something?


Thanks,

Sneha
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] [FreeSurfer] WM Parcellation

[VA Research]

thank you for that,

but i'm confused on how to do the rest as well .

I now have the wmparc2 with unsegmented areas,

how can we create the lobar regions and use those to parcelate the WM into

lobar regions?

On Wed, Jan 27, 2016 at 2:57 PM, Douglas N Greve 
wrote:

> You can regenerate a wmparc that does not have the unsegmented wm with
> something like
>
> cd $SUBJECTS_DIR/subject
> mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
> --volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o mri/wmparc2.mgz
>
> Then create your lobes from that
>
>
> On 01/27/2016 05:47 PM, VA Research wrote:
> > Hello FS experts,
> >
> > Does anyone have some form of step-by-step instructions on how to do
> > this ?
> >
> > Thanks so much
> >
> > Joseph
> > Brainiac . wrote:
> > >/Hi All, />//>/I need to classify WM into different lobes (temporal,
> parietal, />/frontal, occipital). I tried to do the lobe mapping using
> />/parcellations from wmparc.mgz. />/
> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation />//>/My
> problem is the "unsegmented white matter" in wmparc.mgz. My
> />/understanding is that these unsegmented areas are classified so
> />/because they are beyond 5mm from any pre-classified cortex area.
> />//>/My questions: />/(1) So in order to classify "unsegmented WM" into
> lobes, do I need to />/take each voxel in the unsegmented WM region and
> then assign it to the />/closest cortex area to classify it into respective
> parcellations. Then />/re-group into lobes. Is this correct? /
> > >//>/(2) Are there any tailor made function or any other easier way to
> do />/this? Is there any easier way to segment WM into lobes directly that
> I />/have missed? />//>/Thanks, />/Brain/
> >
> > You can do this in a couple of steps. First, you'll need to create a
> > lobe annotation. You can do this in 3 ways:
> > 1. mri_annotation2label --lobesStrict
> >2. mri_annotation2label --lobes
> >3. Custom: break up annotation and recombine:
> >a. mri_annotation to create separate label files
> >b. mri_mergelabels to create single label files for each lobe
> label
> >c. mris_label2annot to create the lobe annotation
> >
> > Next, create the WM segmentation with mri_aparc2aseg, specifying your
> > new lobe annot and adding --labelwm. You can control the distance  with
> > --wmparc-dmax
> >
> > doug
> >
> >
> > ___
> > 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
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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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Re: [Freesurfer] R: Ref FAST and results visualization issue

[Douglas N Greve]

yes, just specfiy the seed you want with the anatomy you want when you 
run mkanalysis-sess

On 01/27/2016 05:27 PM, std...@virgilio.it wrote:
> Briefly, is possible to map the fictional connectivity between a right 
> seed and left cortex?
>
> Stefano
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 27-gen-2016 18.57
> A: 
> Ogg: [Freesurfer] Ref FAST and results visualization issue
>
> Hi list,
>
> I have two requests please.
>
> A- I need to have a reference for FS-FAST (seed based analysis on
> rs data)
>
> B- I have difficulties for results visualization.
>
> How can I do to visualize the the cortical areas which are
> functionally connected with the controlateral seed?
>
>
> For example, my seed are right and left amygdala.
> To visualize RIGHT amygdala - RIGHT cortex connectivity I'm doing:
>
> cd my-group/fc.ramgseed.surf.lh/R_Amygdala
>
>
> tksurfer fsaverage rh inflated -aparc -overlay
> my-glm.wls/intercept/sig.nii.gz
>
> and all is fine.
>
> To visualize RIGHT amygdala - LEFT cortex connectivity I'm doing:
>
> tksurfer fsaverage lh inflated -aparc -overlay
> my-glm.wls/intercept/sig.nii.gz
>
> but the image is so confused. It seem to be the translated image
> which I have projected in the right semi.
>
>
> Thanks
>
>
> Stefano
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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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Re: [Freesurfer] mail option to email custom status of job completion

[Douglas N Greve]

no, sorry, that is hard coded.

On 01/27/2016 06:49 PM, Sneha Pandya wrote:
>
>
> Dear experts,
>
>
> I usually setup batch jobs for my studies and use '-mail' option that 
> emails me completion of recon-all with or without errors. Is there a 
> way or any other option that I can use alongside '-mail' to give me 
> custom status message than the usual one which says "recon-all -s XYZ 
> finished without error at ...". For example if I have set up to run 
> subjects XYZ for only autorecon2 stage, I would like it to send me an 
> email message saying "recon-all autorecon-2 finished without error" or 
> something?
>
>
> Thanks,
>
> Sneha
>
>
>
> ___
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-- 
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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
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Re: [Freesurfer] tracula quality assessment dwi_motion.txt units

[Anastasia Yendiki]

Hi Ruth - Apologies for the omission. It's radians, not degrees. I'll 
update the tutorial.


Best,
a.y

On Wed, 27 Jan 2016, Ruth Carper wrote:


What are the units of measure for translation and rotation as output in the 
dwi_motion.txt file from
Tracula? It's not stated in the output file or on the page
http://freesurfer.net/fswiki/FsTutorial/TraculaOutputs
I would have assumed mm and degrees, but the rotation values are consistently 
less than 0.01, which doesn't
seem likely.

--Ruth


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[Freesurfer] Error on Linux

[Ankita Chatterjee]

Hello,
I am trying to run freesurfer on a machine I got access to that has Ubuntu
(14.04) on it. When I run the tutorials and try to run qdec or freeview, I
get this error - qdec.bin: error while loading shared libraries:
libjpeg.so.62: cannot open shared object file: No such file or directory
I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says
libjpeg.so.62 already exists. Any ideas?
I ran tkmedit and tksurfer and those run fine - only freeview and qdec are
giving this error.

Thanks!
Ankita
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[Freesurfer] Fwd: Call for Nominations: OHBM Young Investigator Award in Human Brain Mapping

[Douglas N Greve]

 Forwarded Message 
Subject:Call for Nominations: OHBM Young Investigator Award in Human 
Brain Mapping
Date:   Wed, 27 Jan 2016 12:05:27 -0600
From:   i...@humanbrainmapping.org
Reply-To:   i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu



*Call for Nominations: OHBM Young Investigator Award in Human Brain 
Mapping (formerly Wiley Young Investigator Award)*

The Organization for Human Brain Mapping, is pleased to announce the 
Call for Nominations for the OHBM Young Investigator Award in Human 
Brain Mapping. This award was formerly named the Wiley Young 
Investigator Award and will continue the tradition of recognizing a 
young investigator who has made significant contributions to the field 
of human brain mapping.  The recipient will receive a cash award of 
$4,000 and an engraved plaque.  Both are presented at the 22nd OHBM 
Annual Meeting being held on June 26-30, 2016 in Geneva, Switzerland. 
For additional Annual Meeting information, please visit our website. 


Each nomination should be no more than two pages and must include the 
following:

 1. A brief statement giving the reasons for nomination and commenting
on the nominee's contributions to the field of human brain mapping;
 2. A short biographical statement on the nominee, including: Name; Date
of birth; Present affiliation; Current mailing address; Current
phone, fax and email; Advance professional degrees (including
institutions and dates); List of postdoctoral fellowships,
residencies and professional appointments (including dates of service);
 3. A short list of *most notable* publications; URL of website (if
available)

Nominations may be made by any individual other than the nominee. To be 
eligible for this award, nominees are required to:

 1. Be under 40 years of age on July 1, 2016
 2. Be within 10 years of completing postdoctoral fellowship or
residency on July 1, 2016;
 3. Have made significant contributions to the field of human brain mapping.

Please send nominations by March 18th, 2016, 12:00 PM US Central 
Standard time to: i...@humanbrainmapping.org. 


Nominations will be evaluated with final selections made by the OHBM 
Council.  The recipient of the award will be notified by April 15, 2016.

View a list of past Wiley Young Investigator Award Recipients. 




Organization for Human Brain Mapping (OHBM)
5841 Cedar Lake Road, Suite 204
Minneapolis, MN 55416 USA
i...@humanbrainmapping.org 

www.humanbrainmapping.org 


To opt out of OHBM emails, contact the OHBM Executive Office at 
i...@humanbrainmapping.org 
.
 


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[Freesurfer] Ref FAST and results visualization issue

[stdp82]

Hi list, 
I have two requests please.
A- I need to have a reference for FS-FAST (seed based analysis on rs data)
B- I have difficulties for results visualization. How can I do to visualize the 
the cortical areas which are functionally connected with the controlateral 
seed? 
For example, my seed are right and left amygdala.To visualize RIGHT amygdala - 
RIGHT cortex connectivity I'm doing:
cd my-group/fc.ramgseed.surf.lh/R_Amygdala
tksurfer fsaverage rh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz

and all is fine.
To visualize RIGHT amygdala - LEFT cortex connectivity I'm doing:

tksurfer fsaverage lh inflated -aparc -overlay my-glm.wls/intercept/sig.nii.gz

but the image is so confused. It seem to be the translated image which I have 
projected in the right semi.

Thanks

Stefano___
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Re: [Freesurfer] recon -all errors

[Jasmin Alves]

Hi Bruce,

 Could you elaborate on what you mean I need to specify the input volume?

Thanks,
Jasmin

On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> if this is the first time you have run this subject (that is, the subject
> dir doesn't exist within $SUBJECTS_DIR), you still need to specify the
> input volume with -i  T1_original_joya.nii
>
> cheers
> Bruce
>
>
> On Tue, 26 Jan 2016, Jasmin Alves wrote:
>
> Bruce,
>> Sorry to be a pain, but for some reason, I cannot still get recon-all to
>> work.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &
>>
>> [1] 14655
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR
>> /Desktop/Brain_Child_subs does not exist.
>>
>> Thanks,
>>
>> Jasmin
>>
>>
>> On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl > >
>> wrote:
>>   Hi Jasmin
>>
>>   you need a '-' sign first. It should be:
>>
>>   recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii
>>   -subject \
>>   joya -all &
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 25 Jan 2016, Jasmin Alves wrote:
>>
>> Hi Bruce,
>> Thanks for the reply, I attempted to direct
>> Subjects_dir to the folder with
>> my data but I received the following error.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> export
>> SUBJECTS_DIR=/Desktop/Brain_Child_subs
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii
>> -subject joya all &
>>
>> [1] 13867
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> ERROR: Flag all
>> unrecognized.
>>
>> -sd /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii -subject joya all
>>
>> Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin
>> Kernel Version 14.5.0: Tue
>> Sep  1 21:23:09 PDT 2015;
>> root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>>
>> recon-all -s joya exited with ERRORS at Mon Jan 25
>> 21:12:58 PST 2016
>>
>> Thanks so much,
>>
>> Jasmin
>>
>>
>> On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Jasmin
>>
>>   you  need to create a directory where you have
>> write permission
>>   and room for the subject reconstruction to be
>> written to, then
>>   set the SUBJECTS_DIR environment variable to
>> point to it. At the
>>   moment you are trying to use the subject
>> directory we
>>   distribute, which is in some system (and
>> read-only) location.
>>   You can do this on the command line of
>> recon-all via:
>>
>>   recon-all -sd  ...
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 24 Jan 2016, Jasmin Alves wrote:
>>
>>   Hello Freesurfer,
>>
>>   I am trying to learn freesurfer and ran into
>> the following
>>   issues below
>>   running the recon -all command.
>>
>>   FREESURFER_HOME: /Applications/freesurfer
>>
>>   Build stamp:
>> freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>>   Kernel info: Darwin 14.5.0 x86_64
>>
>> 1)
>>
>>   joya
>>
>>2)
>>
>>Jasmins-MacBook-Pro:subjects jasminalves$
>> recon-all -i
>>   T1_original_joya.nii
>>   -subject joya -all &
>>
>>
>>   3)
>>
>>   [1] 12300
>>
>>   Jasmins-MacBook-Pro:subjects jasminalves$
>> mkdir:
>>   /Applications/freesurfer/subjects/joya:
>> Permission denied
>>
>>   mkdir:
>> /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   mkdir:
>> /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   cp:
>>
>>
>> /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   cat:
>>
>>
>> /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   INFO: FreeSurfer build stamps do not match
>>
>>   Subject Stamp:
>>
>>   

Re: [Freesurfer] How YOU can help FreeSurfer

[Douglas N Greve]

Thanks to all who have filled out the survey! If you have not done so 
yet, please consider doing so today.
thanks!
doug



On 01/25/2016 06:41 PM, Douglas N Greve wrote:
> We are in the process of preparing a grant to support FreeSurfer 
> development and maintenance:
> Title: FreeSurfer Development, Maintenance, and Hardening.
> PIs: Greve and Fischl.
>
> Grant reviewers need to know that FreeSurfer is useful to a lot of 
> people, so we encourage you to do one of two things:
>
> (1) fill out the form below (probably takes less than 1min) or
> (2) write a letter of support on your institution's letterhead 
> including the information requested on the form and send to 
> gr...@nmr.mgh.harvard.edu
>
> Feel free to forward this survey to others who might not be on the 
> FreeSurfer mailing list (but use FS)
> Please respond by Friday Jan 29.
> Thanks!
> doug
>
> https://docs.google.com/forms/d/1FreWjajItomNlmq190TYl7IS3kPXrHViPJQfjAlg2A0/viewform?c=0=1=mail_form_link
>  
>
>

-- 
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
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Re: [Freesurfer] recon-all segmentation error

[Bruce Fischl]

Hi Jaiashre.

looks like you created a huge topological defect with your edits. Check out 
the ?h.orig.nofix and ?h.inflated.nofix to see what happened.


cheers
Bruce


On Wed, 27 Jan 2016, Jaiashre Sridhar wrote:


Hello,
We made changes to the aseg.mgz in the caudate, nucleus accumbens and
ventricular region using Freeview. We are interested in getting the caudate
volume. We used the following recon options in FreeSurfer
v5.1.0: -autorecon2 –noaseg –autorecon3 
Out of the 60 subjects that we ran, 4 exited with errors. I have provided
the recon-all.log files.
(1) 
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
mhtVoxelList_Add(204, 160, 213, 229294): complete list too big!
..
(2) 
CORRECTING DEFECT 6 (vertices=43037, convex hull=2066)
Segmentation fault
(3) 
mri_fill: could not find pons
find_cutting_plane:seed point not in structure! Searching neighborhood..
(4)  
CORRECTING DEFECT 0 (vertices=96569, convex hull=3716)
Excessive topologic defect encountered: could not allocate 980957071 edges
for retessellation
Cannot allocate memory

Any help is greatly appreciated!
Thanks,
Jaiashre. 

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Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

oh, I take it back. It looks like the SUBJECTS_DIR you pointed it at didn't 
exist. Create it first with


mkdir /Desktop/Brain_Child_subs

then try rerunning.
Bruce


On Wed, 27 Jan 2016, Jasmin Alves wrote:


Hi Bruce,
 Could you elaborate on what you mean I need to specify the input volume? 

Thanks,
Jasmin

On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl 
wrote:
  Hi Jasmin

  if this is the first time you have run this subject (that is,
  the subject dir doesn't exist within $SUBJECTS_DIR), you still
  need to specify the input volume with -i  T1_original_joya.nii

  cheers
  Bruce

  On Tue, 26 Jan 2016, Jasmin Alves wrote:

Bruce,
Sorry to be a pain, but for some reason, I cannot
still get recon-all to
work. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii
-subject joya -all &

[1] 14655

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
ERROR: SUBJECTS_DIR
/Desktop/Brain_Child_subs does not exist.

Thanks,

Jasmin


On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl

wrote:
      Hi Jasmin

      you need a '-' sign first. It should be:

      recon-all -sd /Desktop/Brain_Child_subs -i
T1_original_joya.nii
      -subject \
      joya -all &

      cheers
      Bruce

      On Mon, 25 Jan 2016, Jasmin Alves wrote:

            Hi Bruce, 
            Thanks for the reply, I attempted to
direct
            Subjects_dir to the folder with
            my data but I received the following
error. 

            Jasmins-MacBook-Pro:Brain_Child_subs
jasminalves$
            export
            SUBJECTS_DIR=/Desktop/Brain_Child_subs

            Jasmins-MacBook-Pro:Brain_Child_subs
jasminalves$
            recon-all -sd
            /Desktop/Brain_Child_subs -i
T1_original_joya.nii
            -subject joya all &

            [1] 13867

            Jasmins-MacBook-Pro:Brain_Child_subs
jasminalves$
            ERROR: Flag all
            unrecognized.

            -sd /Desktop/Brain_Child_subs -i
            T1_original_joya.nii -subject joya all

            Darwin Jasmins-MacBook-Pro.local 14.5.0
Darwin
            Kernel Version 14.5.0: Tue
            Sep  1 21:23:09 PDT 2015;
            root:xnu-2782.50.1~1/RELEASE_X86_64
x86_64

            recon-all -s joya exited with ERRORS at
Mon Jan 25
            21:12:58 PST 2016

            Thanks so much,

            Jasmin


            On Mon, Jan 25, 2016 at 6:33 AM, Bruce
Fischl
            
            wrote:
                  Hi Jasmin

                  you  need to create a directory
where you have
            write permission
                  and room for the subject
reconstruction to be
            written to, then
                  set the SUBJECTS_DIR environment
variable to
            point to it. At the
                  moment you are trying to use the
subject
            directory we
                  distribute, which is in some
system (and
            read-only) location.
                  You can do this on the command
line of
            recon-all via:

                  recon-all -sd 
...

                  cheers
                  Bruce


                  On Sun, 24 Jan 2016, Jasmin Alves
wrote:

                  Hello Freesurfer,

                  I am trying to learn freesurfer
and ran into
            the following
                  issues below
                  running the recon -all command. 

                  FREESURFER_HOME:
/Applications/freesurfer

                  Build stamp:
            freesurfer-Darwin-lion-stable-pub-v5.3.0

                  Kernel info: Darwin 14.5.0 x86_64

                    1) 

                  joya

   

Re: [Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

[Douglas N Greve]

I don't know how that could have happened.  Is the geometry of the 
exvivo input oriented correctly? Ie, if you load the orig.mgz into 
freeview or tkmedit, is sag actually sagital, etc?

On 01/26/2016 06:08 PM, John Plass wrote:
> Hi Bruce,
> Thanks for your reply. The orientation is correct in freeview, 
> although, digging further, I see that that it is misoriented when I 
> view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal 
> --surf orig, and the orig volume is shown oriented correctly, but the 
> orig surface appears to have some of the dimensions swapped. Any idea 
> why this might be?
>
> Thanks for your help!
>
> John
>
> On Tuesday, January 26, 2016, Bruce Fischl  > wrote:
>
> Hi John
>
> does it come up in the correct orientation in freeview? If you didn't
> scan it in the orientation that a person would have been lying in the
> scanner, you will need to reorient the data so that we know what e.g.
> anterior is
>
> cheers
> Bruce
>
> On Tue, 26 Jan 2016, John Plass wrote:
>
> > Hello,
> > I've been following the Ex-Vivo Recon instructions
> > https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an
> MPRAGE scan
> > of a formalin-fixated brain. With considerable manual editing,
> I've been
> > able to produce convincing white and pial surfaces, but I am
> having trouble
> > getting a good parcellation. The labels are reversed from
> anterior to
> > posterior (e.g., superior parietal lobule area is labelled as
> middle frontal
> > gyrus). I am assuming this has to do with problems with the surface
> > registration. Also, when viewing the surfaces in Freeview, they
> appear
> > pretty dark (perhaps similar
> 
> tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm
> 
> 
> > l), although the correspondence between red/green and gyri and
> sulci appears
> > to be correct. Might this be part of the problem?
> >
> > Any advice would be much appreciated! If you'd like to take a
> look at the
> > files, please let me know what and where to upload.
> >
> > Thanks very much for your help.
> >
> > Best regards,
> > John Plass
> >
> >
> ___
> 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.
>
>
>
> -- 
>
> ---
> John Plass
> Ph.D. Candidate
> Visual Perception, Neuroscience, and Cognition Lab
> Northwestern University
>
>
>
> ___
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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
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] tracula quality assessment dwi_motion.txt units

[Ruth Carper]

Anastasia,
Thanks for the quick reply.And millimeters for the translation?

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Re: [Freesurfer] recon -all errors

[Jasmin Alves]

This directory already exists. I had already made it, which is why I am
confused that it cannot be found.

On Wed, Jan 27, 2016 at 10:43 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> oh, I take it back. It looks like the SUBJECTS_DIR you pointed it at
> didn't exist. Create it first with
>
> mkdir /Desktop/Brain_Child_subs
>
> then try rerunning.
> Bruce
>
>
>
> On Wed, 27 Jan 2016, Jasmin Alves wrote:
>
> Hi Bruce,
>>  Could you elaborate on what you mean I need to specify the input volume?
>>
>> Thanks,
>> Jasmin
>>
>> On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl > >
>> wrote:
>>   Hi Jasmin
>>
>>   if this is the first time you have run this subject (that is,
>>   the subject dir doesn't exist within $SUBJECTS_DIR), you still
>>   need to specify the input volume with -i  T1_original_joya.nii
>>
>>   cheers
>>   Bruce
>>
>>   On Tue, 26 Jan 2016, Jasmin Alves wrote:
>>
>> Bruce,
>> Sorry to be a pain, but for some reason, I cannot
>> still get recon-all to
>> work.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii
>> -subject joya -all &
>>
>> [1] 14655
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
>> ERROR: SUBJECTS_DIR
>> /Desktop/Brain_Child_subs does not exist.
>>
>> Thanks,
>>
>> Jasmin
>>
>>
>> On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Jasmin
>>
>>   you need a '-' sign first. It should be:
>>
>>   recon-all -sd /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii
>>   -subject \
>>   joya -all &
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 25 Jan 2016, Jasmin Alves wrote:
>>
>> Hi Bruce,
>> Thanks for the reply, I attempted to
>> direct
>> Subjects_dir to the folder with
>> my data but I received the following
>> error.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs
>> jasminalves$
>> export
>> SUBJECTS_DIR=/Desktop/Brain_Child_subs
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs
>> jasminalves$
>> recon-all -sd
>> /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii
>> -subject joya all &
>>
>> [1] 13867
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs
>> jasminalves$
>> ERROR: Flag all
>> unrecognized.
>>
>> -sd /Desktop/Brain_Child_subs -i
>> T1_original_joya.nii -subject joya all
>>
>> Darwin Jasmins-MacBook-Pro.local 14.5.0
>> Darwin
>> Kernel Version 14.5.0: Tue
>> Sep  1 21:23:09 PDT 2015;
>> root:xnu-2782.50.1~1/RELEASE_X86_64
>> x86_64
>>
>> recon-all -s joya exited with ERRORS at
>> Mon Jan 25
>> 21:12:58 PST 2016
>>
>> Thanks so much,
>>
>> Jasmin
>>
>>
>> On Mon, Jan 25, 2016 at 6:33 AM, Bruce
>> Fischl
>> 
>> wrote:
>>   Hi Jasmin
>>
>>   you  need to create a directory
>> where you have
>> write permission
>>   and room for the subject
>> reconstruction to be
>> written to, then
>>   set the SUBJECTS_DIR environment
>> variable to
>> point to it. At the
>>   moment you are trying to use the
>> subject
>> directory we
>>   distribute, which is in some
>> system (and
>> read-only) location.
>>   You can do this on the command
>> line of
>> recon-all via:
>>
>>   recon-all -sd 
>> ...
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 24 Jan 2016, Jasmin Alves
>> wrote:
>>
>>   Hello 

[Freesurfer] 3 years Post Doc position at the Neurofunctional Imaging Group in Bordeaux - France

[Fabrice Crivello]

Dear all,

Please find enclose a 3 years Post Doctoral position that may be of interest.

Post Doc in data processing and databasing of large neuroimaging datasets.

The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research team of 
the Neurodegenerative Disease Institute, UMR 5293 at Bordeaux University. The 
GIN is a multidisciplinary research team gathering scientists with training in 
instrumentation, cognitive neurosciences, signal processing and databasing.
The GIN is a partnering member of the MULTI-LATERAL (Multi-level Integrative 
Analysis of Brain Lateralization for Language, 
http://flagera.eu/?q=FLAG-ERA-call-2015-projects 
) project funded by the 
FLAG-ERA European consortium set up to contribute to the construction of the 
Human Brain Project Flagship project. This partnership aims to identify the 
anatomical, functional and genetic determinants of brain lateralization for 
language functions.

Within this context, the GIN offers a 3 years Post Doc / Research Engineer 
position immediately available.

The core work of the Post Doc will to extract accurate structural and intrinsic 
connectivity asymmetry phenotypes across a range of large scale imaging 
datasets:

First, the post-doc will contribute to develop improved methods and dedicated 
software to reliably and automatically measure individual differences in 
lateralization for anatomy and resting state intrinsic connectivity.

In a second phase, the Post Doc will apply the methods in brain imaging 
datasets (about 10 000 subjects, including the BIL, BIG, I-Share and 
UK-biobank neuroimaging databases) having genetic data available, for the 
purposes of association and rare variant analysis followed by integrated 
genome-level analysis with transcriptomic (lateralized gene expression) dataand 
genomic gene-set analysis.

The applicant will benefit from the support of existing research in this topic 
area and preliminary works in the accurate definition of both structural and 
resting state asymmetry characterization together with data management of large 
neuroimaging cohorts. 

The qualified applicant should have a PhD (or equivalent) in neuro-image 
analysis, computer science (signal and/or image processing) or related field 
and a strong background / experience in neuroimaging data processing. 
Applicants should have experience with tools for analysis of neuroimaging data 
(Freesurfer, SPM,…) and a relevant programming experience (Unix, C/C++ / 
python, MATLAB).

For further information, please contact Dr. Fabrice Crivello 
(fabrice.crive...@u-bordeaux.fr ). 
Salary is according to Bordeaux University salary grid depending on applicant 
experience. The position is limited for 3 years. Job location is in Bordeaux - 
France.

Interested candidates should send their applications including CV with 
publication list and recommendation letters (names and contact information) and 
a written summary of research interests to fabrice.crive...@u-bordeaux.fr 
.
Dr Fabrice CRIVELLO
Mob : +33 (0)6 81 06 47 53
Tel : +33 (0)5 47 30 44 03 
Fax : +33 (0)5 47 30 43 94
https://www.researchgate.net/profile/Fabrice_Crivello

IMN, Institut des Maladies Neurodégénératives, UMR 5293
Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université 
de Bordeaux
Université de Bordeaux
146 rue Léo Saignat - CS 61292 - Case 28
33 076 Bordeaux cedex
http://www.imn-bordeaux.org/

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[Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Erik Lindberg]

Dear Bruce and Freesufers,



I tried to run the command  and then to load it as an overlay - however I
get nothing on the surface of the fsaverage brain. The program is telling
me that it is including x-number of voxels into the mask but when I check I
see nothing on the surface. What is going wrong here?



Further the approach you proposed doing fMRI on the surface sounds
interesting – but I have never used this approach. Could you give me a hint
on the steps I need to take in order to do this?



Thanks in advance!

Eric


yes, but do you want to do the fMRI analysis on the surface or in the
volume? There are lots of advantages to doing it on the surface. If your
sig.cluster.mgh was a surface overlay then the threholded.mgh might be
exactly what you want. Load it on an inflated surface and take a look

cheers
Bruce
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Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

if this is the first time you have run this subject (that is, the subject 
dir doesn't exist within $SUBJECTS_DIR), you still need to specify the 
input volume with -i  T1_original_joya.nii


cheers
Bruce

On Tue, 26 Jan 2016, Jasmin Alves wrote:


Bruce,
Sorry to be a pain, but for some reason, I cannot still get recon-all to
work. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &

[1] 14655

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR
/Desktop/Brain_Child_subs does not exist.

Thanks,

Jasmin


On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl 
wrote:
  Hi Jasmin

  you need a '-' sign first. It should be:

  recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii
  -subject \
  joya -all &

  cheers
  Bruce

  On Mon, 25 Jan 2016, Jasmin Alves wrote:

Hi Bruce, 
Thanks for the reply, I attempted to direct
Subjects_dir to the folder with
my data but I received the following error. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
export
SUBJECTS_DIR=/Desktop/Brain_Child_subs

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii
-subject joya all &

[1] 13867

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
ERROR: Flag all
unrecognized.

-sd /Desktop/Brain_Child_subs -i
T1_original_joya.nii -subject joya all

Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin
Kernel Version 14.5.0: Tue
Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

recon-all -s joya exited with ERRORS at Mon Jan 25
21:12:58 PST 2016

Thanks so much,

Jasmin


On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl

wrote:
      Hi Jasmin

      you  need to create a directory where you have
write permission
      and room for the subject reconstruction to be
written to, then
      set the SUBJECTS_DIR environment variable to
point to it. At the
      moment you are trying to use the subject
directory we
      distribute, which is in some system (and
read-only) location.
      You can do this on the command line of
recon-all via:

      recon-all -sd  ...

      cheers
      Bruce


      On Sun, 24 Jan 2016, Jasmin Alves wrote:

      Hello Freesurfer,

      I am trying to learn freesurfer and ran into
the following
      issues below
      running the recon -all command. 

      FREESURFER_HOME: /Applications/freesurfer

      Build stamp:
freesurfer-Darwin-lion-stable-pub-v5.3.0

      Kernel info: Darwin 14.5.0 x86_64

        1) 

      joya

       2) 

       Jasmins-MacBook-Pro:subjects jasminalves$
recon-all -i
      T1_original_joya.nii
      -subject joya -all &


      3)

      [1] 12300 

      Jasmins-MacBook-Pro:subjects jasminalves$
mkdir:
      /Applications/freesurfer/subjects/joya:
Permission denied

      mkdir:
/Applications/freesurfer/subjects/joya/scripts:
      Permission denied

      mkdir:
/Applications/freesurfer/subjects/joya/scripts:
      Permission denied

      cp:
     
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
      No such
      file or directory

      cat:
     
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
      No such
      file or directory

      INFO: FreeSurfer build stamps do not match

      Subject Stamp: 

      Current Stamp:
freesurfer-Darwin-lion-stable-pub-v5.3.0

      INFO: SUBJECTS_DIR is
/Applications/freesurfer/subjects

      Actual FREESURFER_HOME
/Applications/freesurfer

      /Applications/freesurfer/subjects/joya: No
such file or
      directory.


      [1]+  Exit 1                  recon-all -i
      T1_original_joya.nii -subject
      joya -a

      Thank you,Jasmin

Jasmin 

Re: [Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

[Bruce Fischl]

Hi Erik

did you get any error messages? Did you try changing the thresholds 
(using the "configure overlay" button, or something like that)?


If you run mri_info on sig.cluster.mgh, what is the output?

cheers
Bruce


On Wed, 27 
Jan 2016, Erik Lindberg wrote:




Dear Bruce and Freesufers,

 

I tried to run the command  and then to load it as an overlay - however I
get nothing on the surface of the fsaverage brain. The program is telling me
that it is including x-number of voxels into the mask but when I check I see
nothing on the surface. What is going wrong here?

 

Further the approach you proposed doing fMRI on the surface sounds
interesting – but I have never used this approach. Could you give me a hint
on the steps I need to take in order to do this? 



Thanks in advance!

Eric 



yes, but do you want to do the fMRI analysis on the surface or in the
volume? There are lots of advantages to doing it on the surface. If your
sig.cluster.mgh was a surface overlay then the threholded.mgh might be
exactly what you want. Load it on an inflated surface and take a look

cheers
Bruce

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Re: [Freesurfer] Reg: CORRECTING DEFECT 126 (vertices=61161, convex hull=14255)

[Bruce Fischl]

Hi Jesu

can you please post this type of question to the FS list so others can 
reply and/or learn from the answer? This defect is too big - the defect 
correction grows quadratically in time with the number of vertices in the 
defect. vertices=61161 means that you have a defect that is about half the 
size of the total surface. You need to look at the ?h.orig.nofix and/or the 
?h.inflated.nofix and figure out what the defect is and correct it by 
either editing the wm.mgz or adding control points. If you can't figure 
this out you can upload the entire subject dir to our ftp site and one of 
us will take a look.


cheers
Bruce


On Wed, 27 Jan 2016, Jesu Kiran 
Spurgen wrote:



Dear Prof. Fischl,
Good Afternoon! I have been running freesurfer for a patient data, and have
to find this retesselalation of defect. I have successful with some data but
for some others it looks frozen even after 4 days. Could you please kindly
suggest what I could do here? How could I get some results overriding this
particular step?  

I would extremely grateful for your kind reply and help. 

Warm regards,


Jesu Kiran Spurgen
Postgraduate Student, Advanced Medical Imaging
KU Leuven, Belgium

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[Freesurfer] Statistical analyses with QDEC

[Francesco Cardinale]

Dear Freesurfer experts,
I have some questions about statistical analyses.

How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX 
version, and its tool QDEC to compare cortical thickness between two groups. I 
would like to use age and sex as nuisance factors. No problem with the age, but 
I don’t see the sex in the list of usable variables if I code it as a 
categorical variable (male / female). On the opposite, If I code it as numbers 
(male = 1, female = 2) I can use it, but how can I declare that it is a factor 
and not a continuous numerical variable? I don’t want that “female” affects the 
fitting of the GLM with a value that means “male” * 2. 
What about the use of other morphometric properties as nuisance factors? For 
example, how could I use sulcality or LGI as nuisance factors? Is it possible 
to use more than one scalar simultaneously?
Similarly to question 2, is it possible to use home-made *.mgh scalars as a 
nuisance factors? How?
Do the command-line tools allow such analyses better than QDEC? Related to my 
questions, which features do they add?
In this field of interest, are there any major advantages coming with 
Freesurfer 6.0?
Thanks a lot and best regards

Cico


Francesco Cardinale, MD

Neurosurgeon
"Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda 
"Ca' Granda"
Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia 

phone 0039 02 64442917 
fax 0039 02 64442868 
e-mail francesco.cardin...@ospedaleniguarda.it 
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[Freesurfer] FreeSurfer Lateral Ventricles Error

[Allison Leigh Rainford]

?Good morning,


I am editing a brain using FreeSurfer version 5.1 and I have a pial and white 
matter boundary issue that persists in the lateral ventricles, specifically 
where the software would draw a boundary between the right and left hemispheres 
of the brain. Upon running it through the recon-all pipeline, it reconstructed 
those ventricle boundaries in a way that the boundaries did not even touch the 
walls of the ventricles and had the boundary lines cutting through the middle 
of the left and right lateral ventricles.


After fully filling the ventricles with 255's on the wm.mgz file (to match the 
general reconstruction of other brains we have worked on), the issue still 
largely persists. The pial and white matter boundaries now more accurately 
follow the outer edges of the ventricles but the boundaries that separate the 
left and right hemisphere are still very messy. This issue can be found in over 
60 slices throughout the brain.


Any and all help is appreciated.


Best,


Allison
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