Re: [Freesurfer] Freesurfer/Freeview help

[Bruce Fischl]

Hi Abbie

you just use the recon-all script from the command line:

recon-all \
-i  \
-sd  \
-s  \
-all

this will take 5-20 hours and at the end will create and populate a 
directory tree with segmented volumes and surfaces
cheers
Bruce

On Mon, 27 Jun 
2016, Abbie McNulty wrote:

> Hi Bruce,
> I am trying to create a mesh of the MRI scans, eventually with imported
> scans, but for now just using the information available through the
> software. How do you work these voxel segmentations? I'm just very new with
> the software.
> 
> Say I import an MRI scan, and I want to cortically segment it in order to
> create a mesh of the volume. What are the steps to do this and how do I
> follow through with each step? I tried to watch the youtube tutorials on the
> Freesurfer youtube, but since they are slides informing of what Freesurfer
> can do and not quite a play-by-play interaction of Freeview, I am stuck.
> 
> Thanks
> 
> Abbie
> 
> On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl 
> wrote:
>   Hi Abbie
>
>   what are you trying to create a mesh of? We supply meshes for
>   the
>   gray/white interface and for the pial surface. We supply voxel
>   segmentations of lots of other things that you could mesh, but
>   we don't
>   by default.
>
>   cheers
>   Bruce
>   On Mon, 27 Jun 2016, Abbie McNulty wrote:
>
>   > Hello,
>   > I am trying to segment a MRI brain in order to create a mesh
>   of the image
>   > into finite elements, but I am very new with
>   Freesurfer/Freeview and am not
>   > familiar with the tools. So far, I have only uploaded
>   brain.mgt from the
>   > bert file that comes with the program. If I wanted to mesh
>   this brain, how
>   > should I proceed? The online tutorials have confused me
>   especially since I
>   > am not sure if I am supposed to be using the terminal or the
>   command window
>   > for a lot of the code commands.
>   >
>   > Any help would be appreciated.
>   >
>   > Thanks!
>   >
>   > Abbie McNulty
>   >
>   > --
>   > Abigail C. McNulty
>   > Stanford University Class of 2018
>   > B.A. Candidate in Bioengineering
>   > Stanford Women's XC/ Track and Field
>   >
>   >
> ___
> 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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> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
> 
> 
> 
> 
> --
> Abigail C. McNulty
> Stanford University Class of 2018
> B.A. Candidate in Bioengineering
> Stanford Women's XC/ Track and Field
> 
>
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Re: [Freesurfer] Stuck on “CORRECTING DEFECT”

[Dan Loewenherz]

Hi Bruce,

Thanks for the tips. I tried playing around with the files for a bit
but didn’t make much progress.

Here’s a link to the full tar/gz’ed subject dir:
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=4ej948sa49s

Thanks!
Dan

On Fri Jun 24 22:22:17 EDT 2016, Bruce Fischl
 wrote:

> Hi Dan
>
> that defect is too big, there must be something wrong. Check to see if the
> surface is connected to dura or across the hemis or something. You can look
> at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects
> are. Then you'll need to correct something once you've figured out why
> there is such a huge defect.
>
> cheers
> Bruce
>
> p.s. if you can't sort this out you can tar and gzip your whole subject dir
> and we will take a look
>
> On Fri, Jun 24, 2016 at 9:15 PM, Dan Loewenherz 
>  wrote:
>>
>> Hi freeserver folks,
>>
>> First time poster here. First off, thanks so much to the folks who
>> work on and make this software available to the public. It seems like
>> pretty incredible tech, from what little I understand of it. :)
>>
>> My problem is that the freesurfer process appears to be stuck on the
>> recon-all command. It’s been sitting at ”CORRECTING DEFECT 0
>> (vertices=96285, convex hull=13916)” for about 10 hours now. Any way
>> to cut that number down or should I just let it keep doing its thing?
>> I’ve pasted all of the output pasted at end of the message.
>>
>> Thanks so much!
>>
>> Dan
>>
>> *
>> INFO: assuming .mgz format
>> $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
>>   $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>> before topology correction, eno=-684 (nv=141228, nf=283824,
>> ne=425736, g=343)
>> using quasi-homeomorphic spherical map to tessellate cortical surface...
>>
>> Correction of the Topology
>> Finding true center and radius of Spherical Surface...done
>> Surface centered at (0,0,0) with radius 100.0 in 14 iterations
>> marking ambiguous vertices...
>> 190731 ambiguous faces found in tessellation
>> segmenting defects...
>> 40 defects found, arbitrating ambiguous regions...
>> analyzing neighboring defects...
>>   -merging segment 2 into 0
>>   -merging segment 5 into 0
>>   -merging segment 8 into 0
>>   -merging segment 14 into 0
>>   -merging segment 25 into 0
>>   -merging segment 28 into 0
>>   -merging segment 20 into 17
>>   -merging segment 29 into 17
>>   -merging segment 36 into 35
>> 31 defects to be corrected
>> 0 vertices coincident
>> reading input surface
>> /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix...
>> reading brain volume from brain...
>> reading wm segmentation from wm...
>> Computing Initial Surface Statistics
>>   -face   loglikelihood: -8.8790  (-4.4395)
>>   -vertex loglikelihood: -7.4039  (-3.7020)
>>   -normal dot loglikelihood: -3.5029  (-3.5029)
>>   -quad curv  loglikelihood: -6.1567  (-3.0783)
>>   Total Loglikelihood : -25.9425
>>
>> CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)

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Re: [Freesurfer] Freesurfer/Freeview help

[Abbie McNulty]

Essentially, once segmentation is achieved, how do you mesh the scans?

On Mon, Jun 27, 2016 at 3:41 PM, Abbie McNulty 
wrote:

> Hi Bruce,
>
> I am trying to create a mesh of the MRI scans, eventually with imported
> scans, but for now just using the information available through the
> software. How do you work these voxel segmentations? I'm just very new with
> the software.
>
> Say I import an MRI scan, and I want to cortically segment it in order to
> create a mesh of the volume. What are the steps to do this and how do I
> follow through with each step? I tried to watch the youtube tutorials on
> the Freesurfer youtube, but since they are slides informing of what
> Freesurfer can do and not quite a play-by-play interaction of Freeview, I
> am stuck.
>
> Thanks
>
> Abbie
>
> On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl 
> wrote:
>
>> Hi Abbie
>>
>> what are you trying to create a mesh of? We supply meshes for the
>> gray/white interface and for the pial surface. We supply voxel
>> segmentations of lots of other things that you could mesh, but we don't
>> by default.
>>
>> cheers
>> Bruce
>> On Mon, 27 Jun 2016, Abbie McNulty wrote:
>>
>> > Hello,
>> > I am trying to segment a MRI brain in order to create a mesh of the
>> image
>> > into finite elements, but I am very new with Freesurfer/Freeview and am
>> not
>> > familiar with the tools. So far, I have only uploaded brain.mgt from the
>> > bert file that comes with the program. If I wanted to mesh this brain,
>> how
>> > should I proceed? The online tutorials have confused me especially
>> since I
>> > am not sure if I am supposed to be using the terminal or the command
>> window
>> > for a lot of the code commands.
>> >
>> > Any help would be appreciated.
>> >
>> > Thanks!
>> >
>> > Abbie McNulty
>> >
>> > --
>> > Abigail C. McNulty
>> > Stanford University Class of 2018
>> > B.A. Candidate in Bioengineering
>> > Stanford Women's XC/ Track and Field
>> >
>> >
>> ___
>> 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.
>>
>>
>
>
> --
> Abigail C. McNulty
> Stanford University Class of 2018
> B.A. Candidate in Bioengineering
> Stanford Women's XC/ Track and Field
>



-- 
Abigail C. McNulty
Stanford University Class of 2018
B.A. Candidate in Bioengineering
Stanford Women's XC/ Track and Field
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Re: [Freesurfer] Freesurfer/Freeview help

[Abbie McNulty]

Hi Bruce,

I am trying to create a mesh of the MRI scans, eventually with imported
scans, but for now just using the information available through the
software. How do you work these voxel segmentations? I'm just very new with
the software.

Say I import an MRI scan, and I want to cortically segment it in order to
create a mesh of the volume. What are the steps to do this and how do I
follow through with each step? I tried to watch the youtube tutorials on
the Freesurfer youtube, but since they are slides informing of what
Freesurfer can do and not quite a play-by-play interaction of Freeview, I
am stuck.

Thanks

Abbie

On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl 
wrote:

> Hi Abbie
>
> what are you trying to create a mesh of? We supply meshes for the
> gray/white interface and for the pial surface. We supply voxel
> segmentations of lots of other things that you could mesh, but we don't
> by default.
>
> cheers
> Bruce
> On Mon, 27 Jun 2016, Abbie McNulty wrote:
>
> > Hello,
> > I am trying to segment a MRI brain in order to create a mesh of the image
> > into finite elements, but I am very new with Freesurfer/Freeview and am
> not
> > familiar with the tools. So far, I have only uploaded brain.mgt from the
> > bert file that comes with the program. If I wanted to mesh this brain,
> how
> > should I proceed? The online tutorials have confused me especially since
> I
> > am not sure if I am supposed to be using the terminal or the command
> window
> > for a lot of the code commands.
> >
> > Any help would be appreciated.
> >
> > Thanks!
> >
> > Abbie McNulty
> >
> > --
> > Abigail C. McNulty
> > Stanford University Class of 2018
> > B.A. Candidate in Bioengineering
> > Stanford Women's XC/ Track and Field
> >
> >
> ___
> 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.
>
>


-- 
Abigail C. McNulty
Stanford University Class of 2018
B.A. Candidate in Bioengineering
Stanford Women's XC/ Track and Field
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Re: [Freesurfer] Freesurfer/Freeview help

[Bruce Fischl]

Hi Abbie

what are you trying to create a mesh of? We supply meshes for the 
gray/white interface and for the pial surface. We supply voxel 
segmentations of lots of other things that you could mesh, but we don't 
by default.

cheers
Bruce
On Mon, 27 Jun 2016, Abbie McNulty wrote:

> Hello,
> I am trying to segment a MRI brain in order to create a mesh of the image
> into finite elements, but I am very new with Freesurfer/Freeview and am not
> familiar with the tools. So far, I have only uploaded brain.mgt from the
> bert file that comes with the program. If I wanted to mesh this brain, how
> should I proceed? The online tutorials have confused me especially since I
> am not sure if I am supposed to be using the terminal or the command window
> for a lot of the code commands.
> 
> Any help would be appreciated.
> 
> Thanks!
> 
> Abbie McNulty
> 
> --
> Abigail C. McNulty
> Stanford University Class of 2018
> B.A. Candidate in Bioengineering
> Stanford Women's XC/ Track and Field
> 
>
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[Freesurfer] Freesurfer/Freeview help

[Abbie McNulty]

Hello,

I am trying to segment a MRI brain in order to create a mesh of the image
into finite elements, but I am very new with Freesurfer/Freeview and am not
familiar with the tools. So far, I have only uploaded brain.mgt from the
bert file that comes with the program. If I wanted to mesh this brain, how
should I proceed? The online tutorials have confused me especially since I
am not sure if I am supposed to be using the terminal or the command window
for a lot of the code commands.

Any help would be appreciated.

Thanks!

Abbie McNulty

-- 
Abigail C. McNulty
Stanford University Class of 2018
B.A. Candidate in Bioengineering
Stanford Women's XC/ Track and Field
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Re: [Freesurfer] Question about FreeSurfer

[Dorsa Haji Ghaffari]

Hi,

I need patient specific brain models created by warping atlases to
individual MRIs. I want the model to include the Subthalamic Nucleus, Gpi,
Thalamus and their surrounding organs. (Cortical segmentation is not
necessary). When I use the" recon all "command on one MRI image, I get the
error "cannot find mri.dcm". I have copied the MRI in Freesurfer Home
directory. I really appreciate it if you can help me with that.

Thank you

Dorsa Ghaffari

On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl 
wrote:

> Hi Dorsa
>
> what specific models do you need? The 10-20 hours is to process the data
> from a single subject at a single timepoint. If you check out our wiki
> (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and
> sample datasets and such
>
> cheers
> Bruce
>
> On Mon, 27 Jun 2016, Dorsa Haji
> Ghaffari wrote:
>
> > Hi,
> > I am graduate student at the University of Michigan and I am performing
> > research on deep brain stimulation. I want to warp an anatomical brain
> atlas
> > to individual patient MRIs to get the patient specific brain models out
> of
> > it. I chose FreeSurfer to do this and I have installed it on my
> computer. I
> > realized that it takes 10-20 hrs to reconstruct the image. I wanted to
> ask
> > if that is the time for one image? or the whole series of images?
> > I also wanted to ask if there is a step by step tutorial on how to do
> this.
> >
> > Thank you
> >
> > Dorsa Ghaffari
> >
> >
> >
> >
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>
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Re: [Freesurfer] Question about FreeSurfer

[Bruce Fischl]

Hi Dorsa

what specific models do you need? The 10-20 hours is to process the data 
from a single subject at a single timepoint. If you check out our wiki 
(http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and 
sample datasets and such

cheers
Bruce

On Mon, 27 Jun 2016, Dorsa Haji 
Ghaffari wrote:

> Hi,
> I am graduate student at the University of Michigan and I am performing
> research on deep brain stimulation. I want to warp an anatomical brain atlas
> to individual patient MRIs to get the patient specific brain models out of
> it. I chose FreeSurfer to do this and I have installed it on my computer. I
> realized that it takes 10-20 hrs to reconstruct the image. I wanted to ask
> if that is the time for one image? or the whole series of images?
> I also wanted to ask if there is a step by step tutorial on how to do this.
> 
> Thank you
> 
> Dorsa Ghaffari
> 
> 
> 
>
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Re: [Freesurfer] Question about FreeSurfer

[Dorsa Haji Ghaffari]

Hi,

I am graduate student at the University of Michigan and I am performing
research on deep brain stimulation. I want to warp an anatomical brain
atlas to individual patient MRIs to get the patient specific brain models
out of it. I chose FreeSurfer to do this and I have installed it on my
computer. I realized that it takes 10-20 hrs to reconstruct the image. I
wanted to ask if that is the time for one image? or the whole series of
images?
I also wanted to ask if there is a step by step tutorial on how to do this.

Thank you

>
> Dorsa Ghaffari
>
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Re: [Freesurfer] FSFAST- Cerebellum

[Sabin Khadka]

Hi Thomas- On second thought is it valid to simply do if I want average
time series of the cerebellum regions?

fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >>
avgCerebellum.txt

Is this correct?


Cheers,
Sabin Khadka

On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka 
wrote:

> Hi Thomas and Doug-
>
> Thanks for you suggestions. Per your suggestions I performed following
>
> recon-all -i
> $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz
> -subjid Yeo2011_MNI152_FS
>
> recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS
>
> mri_vol2vol --mov
> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> \
> --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
> talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest
>
> mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
> BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
> Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph
>
> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o
> cerebellum_mask_FSSub.nii.gz
>
> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz
> Buckner_atlas_FSSub
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
> fmcpr.anat.nii.gz
>
> mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf
> test.txt
>
> However, I got the following error
> ERROR: must specify a segmentation volume
>
> Am I doing anything wrong here. Do you have any suggestions/fixes?
>
>
> Cheers,
> Sabin Khadka
>
> On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo  wrote:
>
>> Hi Doug, thanks.
>>
>> Hi Sabin, you can use the following steps to transform the Buckner
>> cerebellum atlas to your subject's native anatomical space and then
>> follow Doug's instructions (taken and adapted from another user
>> Bronwyn's email):
>>
>> 1. Run MNI152 1mm template through recon-all
>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>> Yeo2011_MNI152_FS
>>
>> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
>> nonlinear volumetric space
>> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>> BucknerAtlas1mm_FSI.nii.gz --nearest
>>
>> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
>> volumetric space to each subject:
>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
>> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
>>
>> 4. Create a cerebellum gray matter mask in the native subject's space
>> by applying mri_binarize to aparc+aseg.mgz of the subject
>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
>> cerebellum_mask_subjID.nii.gz
>>
>> 5. Using this mask to mask the Buckner cerebellum parcellations
>> fslmaths Buckner2011_atlas_subjID.nii.gz -mas
>> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
>>
>> Regards,
>> Thomas
>>
>> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
>>  wrote:
>> > yes
>> >
>> >
>> >
>> > On 6/24/16 9:19 AM, Thomas Yeo wrote:
>> >>
>> >> Hi Doug,
>> >>
>> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin
>> >> passed in the cerbellum parcellation in the same anatomical space as
>> >> aseg?
>> >>
>> >> --Thomas
>> >>
>> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
>> >>  wrote:
>> >>>
>> >>> After you run preproc-sess, there will be a file called
>> >>> register.dof6.dat.
>> >>> Map fmri into the anatomical space, something like
>> >>>
>> >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>> >>> fmcpr.anat.nii.gz
>> >>>
>> >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>> >>>
>> >>> However, I don't think that the aseg has those cerebellum
>> parcellations.
>> >>>
>> >>> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>> >>>
>> >>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305
>> >>> space. I
>> >>> process my fmri data with
>> >>>
>> >>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
>> -fwhm 6
>> >>> -per-run -stc odd
>> >>> and then to extract ROI time series values I did
>> >>>
>> >>> mri_segstats --annot fsaverage rh aparc --i
>> >>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
>> >>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>> >>>
>> >>> and for cortical time series
>> >>>
>> >>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> >>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
>> >>> --id
>> >>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54
>> --id
>> >>> 58
>> >>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> >>> subCorticalTimeSeries.txt

[Freesurfer] Freeview nightly / dev / beta

[Vincent Koppelmans]

Hello Freesurfer developers,

I am looking for a version of Freeview that recognizes the -noquit flag. 

V 1.0 Build Aug 24 2015 14:50:08 allows this, but is no longer available from 
"ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev 
”. 

I am particularly interested in a Linux version.

Would it be possible to open up access to the beta versions of Freeview to us 
endusers again?

Thanks!

- Vincent


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Re: [Freesurfer] FSFAST- Cerebellum

[Sabin Khadka]

Hi Thomas and Doug-

Thanks for you suggestions. Per your suggestions I performed following

recon-all -i
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz
-subjid Yeo2011_MNI152_FS

recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS

mri_vol2vol --mov
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
\
--s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest

mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph

mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o
cerebellum_mask_FSSub.nii.gz

fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz
Buckner_atlas_FSSub

mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
fmcpr.anat.nii.gz

mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf
test.txt

However, I got the following error
ERROR: must specify a segmentation volume

Am I doing anything wrong here. Do you have any suggestions/fixes?


Cheers,
Sabin Khadka

On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo  wrote:

> Hi Doug, thanks.
>
> Hi Sabin, you can use the following steps to transform the Buckner
> cerebellum atlas to your subject's native anatomical space and then
> follow Doug's instructions (taken and adapted from another user
> Bronwyn's email):
>
> 1. Run MNI152 1mm template through recon-all
> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
> Yeo2011_MNI152_FS
>
> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
> nonlinear volumetric space
> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
> BucknerAtlas1mm_FSI.nii.gz --nearest
>
> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
> volumetric space to each subject:
> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
>
> 4. Create a cerebellum gray matter mask in the native subject's space
> by applying mri_binarize to aparc+aseg.mgz of the subject
> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
> cerebellum_mask_subjID.nii.gz
>
> 5. Using this mask to mask the Buckner cerebellum parcellations
> fslmaths Buckner2011_atlas_subjID.nii.gz -mas
> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
>
> Regards,
> Thomas
>
> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
>  wrote:
> > yes
> >
> >
> >
> > On 6/24/16 9:19 AM, Thomas Yeo wrote:
> >>
> >> Hi Doug,
> >>
> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin
> >> passed in the cerbellum parcellation in the same anatomical space as
> >> aseg?
> >>
> >> --Thomas
> >>
> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
> >>  wrote:
> >>>
> >>> After you run preproc-sess, there will be a file called
> >>> register.dof6.dat.
> >>> Map fmri into the anatomical space, something like
> >>>
> >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
> >>> fmcpr.anat.nii.gz
> >>>
> >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
> >>>
> >>> However, I don't think that the aseg has those cerebellum
> parcellations.
> >>>
> >>> On 6/21/16 5:52 PM, Sabin Khadka wrote:
> >>>
> >>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305
> >>> space. I
> >>> process my fmri data with
> >>>
> >>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
> -fwhm 6
> >>> -per-run -stc odd
> >>> and then to extract ROI time series values I did
> >>>
> >>> mri_segstats --annot fsaverage rh aparc --i
> >>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> >>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
> >>>
> >>> and for cortical time series
> >>>
> >>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> >>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
> >>> --id
> >>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
> >>> 58
> >>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> >>> subCorticalTimeSeries.txt
> >>>
> >>> Now I am not sure as how to extract cerebellum ROIs (time series as
> >>> described in Buckner et.al 2011)? If there are any other additional
> steps
> >>> I
> >>> need to perform ? or if I have to use some other scripts commands
> (other
> >>> than mri_segstats).
> >>>
> >>>
> >>> Cheers,
> >>> Sabin Khadka
> >>>
> >>> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo 
> >>> wrote:
> 
>  Hi Sabin,
> 
>  The structures 601-628 

Re: [Freesurfer] visualizing statistical maps in FreeView

[Ruopeng Wang]

Hi Lars,

Freeview currently does not have this feature. We will add it in the future.

Best,
Ruopeng

> On Jun 27, 2016, at 10:21 AM, Bruce Fischl  wrote:
> 
> Hi Lars
> 
> 
> I'll leave this for Ruopeng.
> 
> cheers
> Bruce
> 
> On Mon, 27 Jun 2016, Lars Morten Rimol wrote:
> 
>> Hi Bruce,
>>  
>> Yes, now it works (my guess is I loaded a single subject surface as template
>> before…) but I don’t find an FDR correction button in the Configure Overlay
>> interface. The fdr threshold can of course be calculated in Matlab but then
>> why not use tksurfer, which provides that functionality it in the
>> interface.  Also: Unlike in tksurfer, the color bar doesn’t seem to reflect
>> the thresholding of the overlay….
>>  
>>  
>> Thanks!
>>  
>> LMR
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Re: [Freesurfer] visualizing statistical maps in FreeView

[Ruopeng Wang]

As to the color bar, would it be possible to send me a screenshot of it? 

Thanks,
Ruopeng

> On Jun 27, 2016, at 10:21 AM, Bruce Fischl  wrote:
> 
> Hi Lars
> 
> 
> I'll leave this for Ruopeng.
> 
> cheers
> Bruce
> 
> On Mon, 27 Jun 2016, Lars Morten Rimol wrote:
> 
>> Hi Bruce,
>>  
>> Yes, now it works (my guess is I loaded a single subject surface as template
>> before…) but I don’t find an FDR correction button in the Configure Overlay
>> interface. The fdr threshold can of course be calculated in Matlab but then
>> why not use tksurfer, which provides that functionality it in the
>> interface.  Also: Unlike in tksurfer, the color bar doesn’t seem to reflect
>> the thresholding of the overlay….
>>  
>>  
>> Thanks!
>>  
>> LMR
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Re: [Freesurfer] Hippocampal Subfields Segmentation

[Iglesias, Eugenio]

Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out 
what’s going on.  But it definitely sounds funny that it is asking for the CTF, 
since this is supposed to be embedded in the executable… I’ll get back to you 
as soon as possible.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 27 Jun 2016, at 15:32, pierre deman 
> wrote:

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio 
> wrote:
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio



Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 27 Jun 2016, at 15:16, pierre deman 
> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library 
(libmwi18n.so for example, it was missing others before that I added on my 
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the 
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon 
> 
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

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Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Hippocampal Subfields Segmentation

[pierre deman]

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio 
wrote:

> Hi everyone,
> you need to install the Matlab 2012b runtime as explained in the wiki:
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
> Cheers,
> Eugenio
>
>
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 27 Jun 2016, at 15:16, pierre deman  wrote:
>
> Hello,
>
> I have similar problem. "
> "Error:Cannot find CTF archive
>
> /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
> the file is here but when I try to execute it, it's always missing some
> library (libmwi18n.so for example, it was missing others before that I
> added on my computer, but it never ends)
> I am on ubuntu 14.04.
> I thought that the problem is linked to the matlab runtime. I installed
> the 2012b. I tried newer version. installed again the 2012b.
>
> Regards,
> Pierre
>
>
> On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon <
> permesh.dhil...@nottingham.ac.uk> wrote:
>
>> Hello FreeSurfer Developers,
>>
>> I’m having issues with the hippocampal subfields segmentation using OS X
>> Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject
>> Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current
>> Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
>>
>> I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
>> getting an error message : Error:CTF file
>> '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
>> failed to open for 'Read' access. Error message: 'Open a zip file for
>> read/modify failed.’
>>
>> The segmented hippocampal files as described on free surfer wiki cannot
>> be found under the subject ‘mri’ folder.
>> I understand other users have complained of a similar issue within the
>> last week.
>>
>> I’d ve grateful if you could assist me with the issue above.
>>
>> Many thanks
>> Permesh
>>
>> This message and any attachment are intended solely for the addressee
>> and may contain confidential information. If you have received this
>> message in error, please send it back to me, and immediately delete it.
>>
>> Please do not use, copy or disclose the information contained in this
>> message or in any attachment.  Any views or opinions expressed by the
>> author of this email do not necessarily reflect the views of the
>> University of Nottingham.
>>
>> This message has been checked for viruses but the contents of an
>> attachment may still contain software viruses which could damage your
>> computer system, you are advised to perform your own checks. Email
>> communications with the University of Nottingham may be monitored as
>> permitted by UK legislation.
>>
>>
>> ___
>> 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.
>>
>>
>
>
> --
> DEMAN Pierre
> Mobile : +33 7 82 57 80 94
> ___
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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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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
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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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> error
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> properly
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>


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Re: [Freesurfer] Hippocampal Subfields Segmentation

[Iglesias, Eugenio]

Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio



Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 27 Jun 2016, at 15:16, pierre deman 
> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library 
(libmwi18n.so for example, it was missing others before that I added on my 
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the 
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon 
> 
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh


This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
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Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

we need more information if you want us to help you. What does "very odd 
mean"? If you do it in .mgz do you get a different answer than in .mnc? 
If so, why not just compute them in .mgz and convert to .mnc at the end?


cheers
Bruce


On Mon, 27 Jun 2016, Trisanna Sprung-Much wrote:


any ideas?
Thanks!

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much
 wrote:
  thanks Bruce - I had found that option for my fsaverage maps and
  it worked.
What about if I am importing probability maps formed as .mnc and
creating overlays from them? The percentages seem to be very odd for
min and max threshold.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
 wrote:
  Hi Trisanna

  if you are using mri_average you can give it -p as the
  first argument and it will compute a percent at the end
  Bruce
  On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote:

  Hi Bruce

  Is there is a way to set the probability of an
  overlay between 0 and 1?
  Would this have to be done when creating the overlay
  using mri_vol2surf?

  thanks

  Trisanna

  --
  Ph.D. CandidateMcGill University
  Integrated Program in Neuroscience
  Psychology


  On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
  
  wrote:
        Hi Trisanna

        the binaries that take mandatory command-line
  arguments (i.e.
        without a -- or - in front of them) require
  all options to be
        given before the mandatory arguments

        cheers
        Bruce

        On Mon, 20 Jun 2016, Trisanna Sprung-Much
  wrote:

              thanks, Bruce. Yes in the end through
  trial and
              error I tried "mri_average -noconform
  input output"
              and it worked. I was
              surprised that I had to put the
  -noconform first as
              normally one can put the argument
  anywhere in the
              command.

              Best

              Trisanna

              --
              Ph.D. CandidateMcGill University
              Integrated Program in Neuroscience
              Psychology


              On Mon, Jun 20, 2016 at 9:27 AM, Bruce
  Fischl
               wrote:
                    yes, your last file on the command
  line should
              be the output file (the average)

                    cheers
                    Bruce

                    On Mon, 20 Jun 2016, Trisanna
  Sprung-Much
              wrote:

                    As a follow-up, here is the
  mri_info for one
              of my overlays in the folder
                    and the output file that
  mri_average seems to
              create (if I don't specify an
                    output and it re-writes my last
  file). The
              dimensions are off:
                    Any ideas?

                    Trisanna


                  
Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_
  f
              sa
                    vee_left/aalf_lh$ mri_info
             
  fsaverage_overlay_aalf_icbm-102_left.mgz 
                    Volume information for
              fsaverage_overlay_aalf_icbm-102_left.mgz
                              type: MGH
                        dimensions: 163842 x 1 x 1
                       voxel sizes: 1., 1.,
  1.
                              type: FLOAT (3)
                               fov: 163842.000
                               dof: 0
                            xstart: -81921.0, xend:
  81921.0
                            ystart: -0.5, yend: 0.5
                            zstart: -0.5, zend: 0.5
                                TR: 0.00 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 =    
                    0.5000
                                  : x_a =   0.,
  y_a =  
              1., z_a =   0., c_a =  
                    -17.5000
                                  : x_s =   0.,
  y_s =  
              0., z_s =   1., c_s =  
                     18.5000

                    talairach xfm : 
                    Orientation   : 

Re: [Freesurfer] visualizing statistical maps in FreeView

[Bruce Fischl]

Hi Lars


I'll leave this for Ruopeng.

cheers
Bruce

On Mon, 27 Jun 2016, Lars Morten Rimol wrote:



Hi Bruce,

 

Yes, now it works (my guess is I loaded a single subject surface as template
before…) but I don’t find an FDR correction button in the Configure Overlay
interface. The fdr threshold can of course be calculated in Matlab but then
why not use tksurfer, which provides that functionality it in the
interface.  Also: Unlike in tksurfer, the color bar doesn’t seem to reflect
the thresholding of the overlay….

 

 

Thanks!

 

LMR


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Re: [Freesurfer] Hippocampal Subfields Segmentation

[pierre deman]

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some
library (libmwi18n.so for example, it was missing others before that I
added on my computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon <
permesh.dhil...@nottingham.ac.uk> wrote:

> Hello FreeSurfer Developers,
>
> I’m having issues with the hippocampal subfields segmentation using OS X
> Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp:
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp:
> freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.
>
> I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep
> getting an error message : Error:CTF file
> '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf'
> failed to open for 'Read' access. Error message: 'Open a zip file for
> read/modify failed.’
>
> The segmented hippocampal files as described on free surfer wiki cannot
> be found under the subject ‘mri’ folder.
> I understand other users have complained of a similar issue within the
> last week.
>
> I’d ve grateful if you could assist me with the issue above.
>
> Many thanks
> Permesh
>
>
>
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please send it back to me, and immediately delete it.
>
> Please do not use, copy or disclose the information contained in this
> message or in any attachment.  Any views or opinions expressed by the
> author of this email do not necessarily reflect the views of the
> University of Nottingham.
>
> This message has been checked for viruses but the contents of an
> attachment may still contain software viruses which could damage your
> computer system, you are advised to perform your own checks. Email
> communications with the University of Nottingham may be monitored as
> permitted by UK legislation.
>
>
> ___
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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
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> dispose of the e-mail.
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>


-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

any ideas?

Thanks!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> thanks Bruce - I had found that option for my fsaverage maps and it worked.
>
> What about if I am importing probability maps formed as .mnc and creating
> overlays from them? The percentages seem to be very odd for min and max
> threshold.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl 
> wrote:
>
>> Hi Trisanna
>>
>> if you are using mri_average you can give it -p as the first argument and
>> it will compute a percent at the end
>> Bruce
>> On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>>>
>>> Is there is a way to set the probability of an overlay between 0 and 1?
>>> Would this have to be done when creating the overlay using mri_vol2surf?
>>>
>>> thanks
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Trisanna
>>>
>>>   the binaries that take mandatory command-line arguments (i.e.
>>>   without a -- or - in front of them) require all options to be
>>>   given before the mandatory arguments
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>>>
>>> thanks, Bruce. Yes in the end through trial and
>>> error I tried "mri_average -noconform input output"
>>> and it worked. I was
>>> surprised that I had to put the -noconform first as
>>> normally one can put the argument anywhere in the
>>> command.
>>>
>>> Best
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl
>>>  wrote:
>>>   yes, your last file on the command line should
>>> be the output file (the average)
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much
>>> wrote:
>>>
>>>   As a follow-up, here is the mri_info for one
>>> of my overlays in the folder
>>>   and the output file that mri_average seems to
>>> create (if I don't specify an
>>>   output and it re-writes my last file). The
>>> dimensions are off:
>>>   Any ideas?
>>>
>>>   Trisanna
>>>
>>>
>>>  Tgtrisanna@kaplan
>>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f
>>> sa
>>>   vee_left/aalf_lh$ mri_info
>>> fsaverage_overlay_aalf_icbm-102_left.mgz
>>>   Volume information for
>>> fsaverage_overlay_aalf_icbm-102_left.mgz
>>> type: MGH
>>>   dimensions: 163842 x 1 x 1
>>>  voxel sizes: 1., 1., 1.
>>> type: FLOAT (3)
>>>  fov: 163842.000
>>>  dof: 0
>>>   xstart: -81921.0, xend: 81921.0
>>>   ystart: -0.5, yend: 0.5
>>>   zstart: -0.5, zend: 0.5
>>>   TR: 0.00 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 =
>>>   0.5000
>>> : x_a =   0., y_a =
>>> 1., z_a =   0., c_a =
>>>   -17.5000
>>> : x_s =   0., y_s =
>>> 0., z_s =   1., c_s =
>>>18.5000
>>>
>>>   talairach xfm :
>>>   Orientation   : RAS
>>>   Primary Slice Direction: axial
>>>
>>>   voxel to ras transform:
>>>   1.   0.   0.
>>> -81920.5000
>>>   0.   1.   0.
>>> -18.
>>>   0.   0.   1.
>>>  18.
>>>   0.   0.   0.
>>> 1.
>>>
>>>   voxel-to-ras determinant 1
>>>
>>>  

[Freesurfer] Hippocampal Subfields Segmentation

[Permesh Dhillon]

Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh




This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it. 

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
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