date:20170809

[Freesurfer] Hippocampus subfield

2017-08-09 Thread Lin, Yizhi

Dear experts in Freesurfer,

I am doing analysis on hippocampus subfield and I'm wondering if I could
obtain cortical thickness data from each segmentation? Thanks so much!

Best,

Ariel
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[Freesurfer] Reporting age differences between groups

2017-08-09 Thread Martin Juneja

Hi,

I need a general advice from the experts out there.

I am comparing cortical measures (thickness and volume) between controls
and patients using FreeSurfer. I used 'age' and 'gender' as covariates (in
fsgd file) while calculating group differences.

I was wondering even if I removed the effects of 'age' and 'gender' for
this comparison, should I perform and report t-test/one way ANOVA results
if there are significant differences in 'age' between the two groups or
there is no need to report 'age' difference results in manuscript,
regardless of being significant or non-significant.

Thanks.
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Re: [Freesurfer] Pial surface editing

2017-08-09 Thread Bruce Fischl

are you sure you created the brainmask with -rl orig.mgz? It should have 
the same dimensions afterwards.


On Wed, 9 Aug 2017, Michelle VanTieghem 
wrote:



-bash-4.1$ mri_info orig.mgz
Volume information for orig.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: 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 =   
-5.2291
              : x_a =   0., y_a =   0., z_a =   1., c_a =   
 3.0505
              : x_s =   0., y_s =  -1., z_s =   0., c_s =   
-0.9364

talairach xfm 
:/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri/transforms/talaira
ch.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.   0.   0.   122.7709
                0.   0.   1.  -124.9495
                0.  -1.   0.   127.0636
                0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:
               -1.   0.   0.   122.7709
               -0.  -0.  -1.   127.0636
               -0.   1.  -0.   124.9495
                0.   0.   0.     1.
---
-
-bash-4.1$ mri_info brainmask.mgz 
Volume information for brainmask.mgz
          type: MGH
    dimensions: 221 x 274 x 261
   voxel sizes: 1., 1., 1.
          type: SHORT (4)
           fov: 274.000
           dof: 0
        xstart: -110.5, xend: 110.5
        ystart: -137.0, yend: 137.0
        zstart: -130.5, zend: 130.5
            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 =   
-5.2291
              : x_a =   0., y_a =  -1., z_a =   0., c_a =   
 3.0505
              : x_s =   0., y_s =   0., z_s =   1., c_s =   
-0.9364

talairach xfm : 
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
               -1.   0.   0.   105.2709
                0.  -1.   0.   140.0505
                0.   0.   1.  -131.4364
                0.   0.   0.     1.

voxel-to-ras determinant 1

ras to voxel transform:
               -1.   0.   0.   105.2709
                0.  -1.   0.   140.0505
               -0.  -0.   1.   131.4364
                0.   0.   0.     1.
---
--
Iterating 2 times
-
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 84 (84), valley at  0 (-1)
csf peak at 42, setting threshold to 70
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
-
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 83 (83), valley at  0 (-1)
csf peak at 41, setting threshold to 69
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating -
writing output to brain.mgz
3D bias adjustment took 4 minutes and 23 seconds.
#
#@# Mask BFS Wed Aug  9 02:03:44 EDT 2017
/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz

threshold mask volume at 5
ERROR: dimension mismatch between source and mask
Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17
EST 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s SB020_fu1 exited with ERRORS at Wed Aug  9 02:03:46 EDT 2017



On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl 
wrote:
  can you send us the output of mri_info on orig.mgz and
  brainmask.mgz created with the -rl flag? And also send us the
  full screen output of the command that fails?

  thanks
  Bruce
   On Wed, 9 Aug 2017, Michelle VanTieghem wrote:

Hi, 
I originally used 
mri_convert orig.mgz afni_stripped_volume.brik
brainmask.mgz 

and I re-did it using  the -rl flag as you
recommended. 

it did not influence anything, same problem. 

I'd appreciate any trouble shooting tips. 

Thanks,
M

On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl

Re: [Freesurfer] convert mgh to nii problems - cannot get output file to reshape properly

2017-08-09 Thread Douglas N Greve

Can you send me the file?


On 08/09/2017 04:17 AM, Suzanne Witt wrote:
> Hi.
>
> I am having a problem similar to that previously described on the freesurfer 
> message boards from May 2011 (Subject: mgh conversion).  Unfortunately, that 
> thread ends with Doug asking the person to send him the files in question, so 
> there does not appear to be any sort of publicly published solution.
>
> I was sent two .mgh files with the resulting activation maps from an fMRI 
> analysis (both left and right hemispheres) and told that the maps were in 
> fsaverage space.  I was not sent any other accompanying files.  I am trying 
> to convert them to nii format.
>
> I have tried both:
>   
> 1. mri_convert filename.mgh filename.nii.gz
>
> and mri_surf2surf (as was suggested in the previous thread)
>
> 2. mri_surf2surf —sval filename.mgh —tval filename.nii —reshape 
> —reshape-factor 6 —s fsaverage —hemi lh
>
> (I realize that the command options should be preceded by double dashes, but 
> my email program is quite insistent about automatically formatting these to 
> long dashes.)
>
> In both cases the when checking the output file using mri_info, the 
> dimensions are still: 163842 x 1 x 1.
>
> Are there any suggestions as to how best to proceed?
>
> Thanks in advance,
>
> Suzanne Witt
>
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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] ROI labeling?

2017-08-09 Thread Douglas N Greve

You can map the ROIs into fsaverage space as binary masks, then average 
them together, then binarize the average (you'd have  to pick the 
threshold). You cannot give mri-glmfit mutliple labels, but you can 
merge the labels together (mri_merge_labels)


On 08/04/2017 03:13 PM, Sadie Marvel wrote:
> Sorry, I meant that I would somehow want to merge all of these masks together 
> into one. Not changing the values in the masks, but somehow combining them.
> Also, with the mri_glmfit --label flag, is it possible to have multiple 
> labels listed (like one label per subject)?
> Sort of like a frame mask where we we want to take into account every 
> subject's individual ROI label.
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Thursday, August 3, 2017 4:55 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] ROI labeling?
>
> what do you mean by an average of the mask? Such an average would not be
> binary.
>
>
> On 08/03/2017 04:30 PM, Sadie Marvel wrote:
>> And what if I wanted to compute just one ROI mask (for each region) that is 
>> an average of all the subjects individual ROI masks?
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Thursday, August 3, 2017 4:15 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] ROI labeling?
>>
>> If you are just going to use them as a mask for mri_glmfit, then you can
>> just pass it as --mask or --label, no need to map it back to the
>> individual (which you could do with mri_surf2surf)
>>
>>
>> On 08/03/2017 04:08 PM, Sadie Marvel wrote:
>>> Hi again Freesurfers,
>>>
>>> I am doing a surface based ROI analysis where for each subject,
>>> isomorphic ROIs of 300 vertices (centered around peak functional
>>> activations) were found on the fsaverage surface space. I was
>>> wondering if I should register these masks that I have created back to
>>> each subject's individual surface before creating labels for these
>>> ROIs, and if so, what would the registration file be to register the
>>> fsaverage space back to each subject's space? The goal of this is to
>>> be able to run mri_glmfit on just the spaces within these labels. Is
>>> there a better method? Also, each subject will have a different number
>>> of labels considering that not every ROI was present on every subject.
>>> will this be a problem when running glmfit?
>>>
>>> Thanks
>>>
>>>
>>>
>>>
>>>
>>> ___
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>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=F2PgY5a-UpmIys4GjIY91-18ok4YKa7QNdxfaZWaA0M=
>> --
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=dNTiTZM2k4H_ZFSLvXIpaHUFlf2j9OsxSfiZbdVVy1Y=
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: 
>> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=-MNH1l23vgFGiXhqvaJyfT33Qag5-ddnxlYIHUU99W0=
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=F2PgY5a-UpmIys4GjIY91-18ok4YKa7QNdxfaZWaA0M=
>>
>>
>> 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
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=C3lAhbV3ZwBBXlYZT58CMcDnypDoDoJZxiTFeHyxq-0=
>>   . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and 
>>

Re: [Freesurfer] Pial surface editing

2017-08-09 Thread Michelle VanTieghem

-bash-4.1$ mri_info orig.mgz
Volume information for orig.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: 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 =
-5.2291
  : x_a =   0., y_a =   0., z_a =   1., c_a =
 3.0505
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
-0.9364

talairach xfm :
/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   122.7709
0.   0.   1.  -124.9495
0.  -1.   0.   127.0636
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.   122.7709
   -0.  -0.  -1.   127.0636
   -0.   1.  -0.   124.9495
0.   0.   0. 1.

-bash-4.1$ mri_info brainmask.mgz
Volume information for brainmask.mgz
  type: MGH
dimensions: 221 x 274 x 261
   voxel sizes: 1., 1., 1.
  type: SHORT (4)
   fov: 274.000
   dof: 0
xstart: -110.5, xend: 110.5
ystart: -137.0, yend: 137.0
zstart: -130.5, zend: 130.5
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 =
-5.2291
  : x_a =   0., y_a =  -1., z_a =   0., c_a =
 3.0505
  : x_s =   0., y_s =   0., z_s =   1., c_s =
-0.9364

talairach xfm :
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
   -1.   0.   0.   105.2709
0.  -1.   0.   140.0505
0.   0.   1.  -131.4364
0.   0.   0. 1.

voxel-to-ras determinant 1

ras to voxel transform:
   -1.   0.   0.   105.2709
0.  -1.   0.   140.0505
   -0.  -0.   1.   131.4364
0.   0.   0. 1.
-
Iterating 2 times
-
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 84 (84), valley at  0 (-1)
csf peak at 42, setting threshold to 70
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
-
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 83 (83), valley at  0 (-1)
csf peak at 41, setting threshold to 69
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating -
writing output to brain.mgz
3D bias adjustment took 4 minutes and 23 seconds.
#
#@# Mask BFS Wed Aug  9 02:03:44 EDT 2017
/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz

threshold mask volume at 5
ERROR: dimension mismatch between source and mask
Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17
EST 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s SB020_fu1 exited with ERRORS at Wed Aug  9 02:03:46 EDT 2017



On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl 
wrote:

> can you send us the output of mri_info on orig.mgz and brainmask.mgz
> created with the -rl flag? And also send us the full screen output of the
> command that fails?
>
> thanks
> Bruce
>
>  On Wed, 9 Aug 2017, Michelle VanTieghem wrote:
>
> Hi,
>> I originally used
>> mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz
>>
>> and I re-did it using  the -rl flag as you recommended.
>>
>> it did not influence anything, same problem.
>>
>> I'd appreciate any trouble shooting tips.
>>
>> Thanks,
>> M
>>
>> On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl 
>> wrote:
>>   what was your mri_convert command line? It should be something
>>   like
>>
>>   mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 7 Aug 2017, Michelle VanTieghem wrote:
>>
>> Hi Bruce,
>>
>> Here is

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Ruopeng Wang

Hmm, if you run:

ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz

what does it show?

> On Aug 9, 2017, at 4:47 PM, Z Hessam  wrote:
> 
> of course:
> 
> hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v 
> bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz 
> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
> bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red 
> bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
> 
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> MRIread failed: Unable to read from 
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> MRIread failed: Unable to read from 
> /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
> mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
>  -1): read error
> 
> thanks a lot for your attention 
> 
> On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang  > wrote:
> Can you copy and paste the exact command line you ran and the error message?
> 
> Ruopeng
> 
> 
> On 08/09/2017 02:21 PM, Z Hessam wrote:
>> 
>> I try it without \ chars, works for some other subjects
>> but it doesn't work for one of them,and now I can even open it with GUI, 
>> while I could open it before.
>> It seems that is time variant!
>> Should I run "recon-all ..." again for that subject?
>> 
>> 
>> 
>> 
>> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl > > wrote:
>> can you try it without all the \ characters?  You shouldn't need them if 
>> it's all on one line
>> 
>> On Wed, 9 Aug 2017, Z Hessam wrote:
>> 
>> 
>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \   
>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> MRIread failed: Unable to read from
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> 
>> 
>> I use the example 4 in the "download and install" page of site
>> 
>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl > >
>> wrote:
>> 
>>   hmmm, that looks ok, but it's hard to tell with all the
>>   backslashes and blank lines and such. Can you send the full
>>   command on a single line (e.g. by hitting up-arrow in the
>>   terminal window) and the actual output of freeview?
>> 
>>On Wed, 9 Aug 2017, Z Hessam wrote:
>> 
>> 
>> Hello Freesurfer Developers,
>> 
>> I have problem when I use "freeview" example code in
>> terminal,
>> freeview -v \
>> 
>> bert/mri/T1.mgz \
>> 
>> bert/mri/wm.mgz \
>> 
>> bert/mri/brainmask.mgz \
>> 
>>
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>> 
>> -f \
>> 
>> bert/surf/lh.white:edgecolor=blue \
>> 
>> bert/surf/lh.pial:edgecolor=red \
>> 
>> bert/surf/rh.white:edgecolor=blue \
>> 
>> bert/surf/rh.pial:edgecolor=red
>> it tell "Failed to load MRI ",
>> mri_read(): couldn't determine type of file
>> 
>> MRIread failed: Unable to read from 
>> mri_read(): couldn't determine type of file
>> 
>> but i can load wm.mgz and other existed files in
>> GUI.
>> 
>> please help me to know why this error happend? and
>> what should I do to solve
>>  this?
>> 
>> I've searched the list, I found a similar errors,
>> but wasn't helpful answer reported.
>> help me please
>> 
>> regards
>> 
>> On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
>> > wrote:
>> 
>> Hello Freesurfer Developers,
>> 
>> I have problem when I use "freeview" example code in
>> terminal,
>> freeview
>> -v \
>> 
>> bert/mri/T1.mgz \
>> 
>> bert/mri/wm.mgz \
>> 
>> bert/mri/brainmask.mgz \
>> 
>>
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>> 
>> -f \
>> 
>> bert/surf/lh.white:edgecolor=blue \
>> 
>> bert/surf/lh.pial:edgecolor=red \
>> 
>>

Re: [Freesurfer] Optseq2 timing outputs

2017-08-09 Thread Douglas N Greve

sorry, I thought I answered this. those slight offsets are not 
important, you can round to nearest TR


On 08/08/2017 10:57 PM, Ruthie Shaffer wrote:
> Hi all,
>
> I sent a message previously and just wanted to check in one more time 
> about this question (apologies for the repeat message!).
>
> I’m using Optseq2 to generate stimulus / jitter schedules and, 
> depending on the TR I use, in the output files I see onset times like 
> 124.4001 (instead of 124.4) or 124.7999 (instead of 124.8).
>
> This is the command I’m using:
> optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 
> --nkeep 6 --o CRtiming.2017 --nsearch 10 --tnullmin 0 --tnullmax 6.4
>
> Should I be concerned about the outputs (does it mean that I’ve 
> specified something incorrectly in the above command), or is it 
> correct to assume that something like 124.4001 just means 124.4?
>
> Anyway, thank you so much for your help on this!
>
> Best wishes,
>
> Ruth Shaffer
>
>
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Re: [Freesurfer] Talairach error

2017-08-09 Thread Douglas N Greve

It is failing the tal registration check. Does the registration look ok? 
If so, then run with -no-talcheck.


On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote:
> Hello FreeSurfer experts,
>
> I have been running into a consistent problem of Talairach alignment 
> error in my recon-all for some of my subjects, even though I was able 
> to get a completed recon-all for other subjects by using the same 
> procedure to obtain my nifti files. I have attached the recon-all logs 
> of a successful and a Talairach failed subject respectively, and as I 
> try to understand the difference, in the successful one this was tried 
> the last: INFO: Trying MINC mritotal to perform Talairach align... 
> then failed, then there is a "New invocation of recon-all " which 
> succeeded. I do not think I made that invocation. Could someone help 
> me figure out what I am missing, and how can I make recon-all continue 
> as I somehow did previously?
>
> Thank you so much!
> Idil
>
>
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Re: [Freesurfer] Freesurfer PIB PET image processing

2017-08-09 Thread Douglas N Greve

We do not have any thing to specifically analyze PiB. You can look at 
the PETsurfer page for more general instructions


On 08/09/2017 02:15 AM, M Janani wrote:
>
> Hi Team,
>
> I apologize, I am new to Freesurfer.
>
> Currently we are processing PIB PET images.
>
> When we compare the SPM data along with FREESURFER 
> outputs. We were able to see a large variation in the values.
>
> Could you please guide us in processing PIB PET images 
> in Freesurfer?
>
> Since the signal of a PET image is very weak, we used 
> MRI image as a guide to map it to Standard brain.
>
> How does Freesurfer process in this case?
>
> Your help would be grateful.
>
> Regards,
>
> Janani
>
>
>
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Re: [Freesurfer] VBM

2017-08-09 Thread Douglas N Greve

we do not support vbm processing

On 08/08/2017 06:21 PM, Shane S wrote:
> Hello Experts,
>
> Can we do VBM in MNI template using the outputs from recon all? Which 
> file should I be using? And how do I smooth the volumes?
>
> Thank you for the tips!
>
> -- 
> Shane S
>
>
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Re: [Freesurfer] Sphere above a certain vetex

2017-08-09 Thread Douglas N Greve

A sphere or a circle? If circel, you can create a delta functon (a map 
on the surface where everything is 0 except your vertex which is 1.0) 
with mri_volsynth, specify the delta column to be your vertex number. 
Then smooth with mris_fwhm, then threshold with mri_binarize at some 
very low value (eg, 1e-6), then visualize this map to see a circle

On 08/08/2017 12:15 PM, Redwan Maatoug wrote:
> Hi everybody,
>
> I have a .annot file  and I would like to display a sphere above one 
> certain vertex.
> (I know the coordinates of the vertex)
>
> Someone knows a way to do that ?
> Thank you very much,
> Redwan
>
>
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Re: [Freesurfer] Generating Surfaces from Labels

2017-08-09 Thread Douglas N Greve



On 08/08/2017 03:42 PM, Zach Humphrey wrote:
> Hello All,
>
> I have been attempting to convert Label files generated using 
> mri_annotation2label into surface files for use in external programs. 
> In order to do this I first need to convert the label files into 
> freesurfer binary. I have attempted to use the mri_label2vol function 
> to generate an mgz file which could then be converted into freesurfer 
> binary but this has resulted in mgz files which depict a solid cube 
> rather than any brain structure. Any ideas as to why this could be?
I don't understand what this means. Can you elaborate or share a pic?
>
> I would also prefer to avoid ever converting the label files to a 
> volume as converting the volume file to a surface file results in a 
> lower quality than if the file has been maintained as a surface file 
> throughout. Is there any way to use the Desikan Atlas to "divide" say 
> the lh.pial surface file and generate a number of .pial files each 
> consisting of one of the regions described by the Desikan Atlas?
>
> Thanks,
> Zachary Humphrey
>
>
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Re: [Freesurfer] ASL with rcbf-prep

2017-08-09 Thread Douglas N Greve

Hi Lauri, this program is not being supported anymore, sorry:)

doug



On 08/08/2017 02:20 PM, Tuominen, Lauri Johannes wrote:
> Dear freesurfers,
>
> I have data collected here at the martinos using the Siemens ep2d_PASL 
> sequence. I run the command "rcbf-prep —s subject —rcbf asl.nii —o tesfolder" 
> or something like that. The resulting rcbf.nii looks good, but the values are 
> negative? Is this just a matter of tag and ref images being in a wrong order 
> and can I just fix it by removing the first image (after the M0)? Or is it 
> more complicated?
>
> Thanks for your help
> Lauri
>   
>
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Re: [Freesurfer] question about effects of changing server and freesurfer versions IF the entire study is consistent

2017-08-09 Thread Douglas N Greve

There will certainly be differences between 5.3 and 6.0. Changing the OS 
will probably have minor effects.


On 08/08/2017 12:24 PM, STACEY M SCHAEFER wrote:
>
> Hello Freesurfer experts,
>
>
> We have processed, hand-edited, and QA'ed over 130 subjects' scans 
> with version 5.3.0 on a linux sci6 box, and extracted the atlas-based 
> ROI values for cortical thickness, volume, curvature, etc. The 
> servers need upgrading but there are still whole brain analyses to 
> run.  Will there be any issues if we have processed all subjects 
> identically, but then run analyses on the data with an upgraded linux 
> and freesurfer's latest version?
>
>
> Thank you for your guidance!
> Stacey
>
> *Stacey M. Schaefer, Ph.D.*
> Center for Healthy Minds
>
> University of Wisconsin-Madison
>
> 625 W Washington Ave
>
> Madison WI 53703
>
> 608-263-9321
>
>
>
>
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Re: [Freesurfer] Matrix ill-conditioned error for dods thickness mri_glmfit analysis

2017-08-09 Thread Douglas N Greve

can you send the design matrix Xg.mtx and the full terminal output?


On 08/08/2017 09:13 AM, Sullivan, Danielle Renee wrote:
>
> Hi FreeSurfer Experts,
>
>
> I am trying to run a dods cortical thickness analysis examining the 
> interaction of group on a continuous variable while controlling for 
> other variables.
>
>
> Specifically, I have 6 classes (gender by three groups [zero, one, 
> two]). I am interested in the group interaction with a continuous 
> variable while controlling for gender (among 4 other continuous 
> variables). I set up my fsgd file (see attached) and contrast file (36 
> dimensions- F test):
>
> *0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -1 0 1 
> -1 0]/2*
>
> *0 0 0 0 0 0 **0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -0 
> -1 1  0 -1]/2*
>
>
> and ran this command:
>
>
> *mri_glmfit --y 
> **lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh
>  
> --fsgd 
> fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt
>  
> dods --C 
> /GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx 
> --surf fsaverage lh --cortex --glmdir 
> lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir
>  
> *
>
>
> But keep getting this error:
>
>
> *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08*
>
> **
>
> *Possible problem with experimental design:*
>
> *Check for duplicate entries and/or lack of range of*
>
> *continuous variables within a class.*
>
> *If you seek help with this problem, make sure to send:*
>
> *  1. Your command line:*
>
> *mri_glmfit --y 
> lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh
>  
> --fsgd 
> fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt
>  
> dods --C 
> /Volumes/VA_Imaging/Projects/salat/2389_TRT/dmiller/GGT_CRP/GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx
>  
> --surf fsaverage lh --cortex --glmdir 
> lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir
>  
> *
>
> *  2. The FSGD file (if using one)*
>
> *  3. And the design matrix above*
>
>
>
> Any idea on what I am doing wrong?
>
>
> Danielle R. Miller, Ph.D.
>
> National Center for PTSD
>
> VA Boston Healthcare System Jamaica Plain
>
> Boston University School of Medicine
>
> OFFICE: (857) 364-4022
>
>
>
>
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Re: [Freesurfer] Extracting pial surface from manually pareclated atlas

2017-08-09 Thread Douglas N Greve

do you mean the pia tissue (which we can't do) or the pial surface, 
which is a surface and not in aparc+aseg


On 08/07/2017 06:59 PM, Almarshad F. wrote:
> Hi freesurfer team
>
> I'm just wondering if there is any way to extract left and right pial from 
> manually parecllated file apar+aseg .mgh
> I need to view them with the new parecellation file
> Thanks in advance
> Fatima
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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
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Re: [Freesurfer] GLM error - cannot read fsgd file for reading

2017-08-09 Thread Douglas N Greve

make sure you pass the full path to the fsgd, otherwise it looks in the 
current folder. Also make sure it is readable by you


On 08/09/2017 05:12 PM, Nick Corriveau-Lecavalier wrote:
>
> Hi Freesurfer team,
>
>
> I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) 
> with 0 covariables at the moment, but I would like to add two 
> eventually. I've been following the tutorial on this link: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write 
> the command it says ''cannot open g3v0.fsgd for reading''.
>
>
> In my /subjects/fsgd file, there is my fsgd file, and my contrast 
> file. Am I missing an additionnal file or something? Is the format of 
> my files correct?
>
>
> If it can help, here's what my fsgd file looks likes:
>
>
> GroupDescriptorFile 1
> Title OSGM
> Class Control
> Class SCD
> Class MCI
> Variables
> Input 3431566 CTL
> Input 3514091 CTL
> Input 4051959 CTL
> Input 4344061 CTL
> Input 4557550 CTL
> Input 7060373 CTL
> Input 7274924 CTL
> Input 7308293 CTL
> Input 7424803 CTL
> Input 7459501 CTL
> Input 7543023 CTL
> Input 7661810 CTL
> Input 8069157 CTL
> Input 8330218 CTL
> Input 8656527 CTL
> Input 8875385 CTL
> Input 9296157 CTL
> Input 3025432 SCD
> Input 3494204 SCD
> Input 3702154 SCD
> Input 3708747 SCD
> Input 3865361 SCD
> Input 4316663 SCD
> Input 4509950 SCD
> Input 4548020 SCD
> Input 4893763 SCD
> Input 5381177 SCD
> Input 5477234 SCD
> Input 5522727 SCD
> Input 6121388 SCD
> Input 6168985 SCD
> Input 6258913 SCD
> Input 6274286 SCD
> Input 6334263 SCD
> Input 6417837 SCD
> Input 6427603 SCD
> Input 7435733 SCD
> Input 7485585 SCD
> Input 7712552 SCD
> Input 8827943 SCD
> Input 8980899 SCD
>
> Regards,
>
>
> Nick Corriveau-Lecavalier, B.Sc. (Hons)
> Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique
> Coordonateur à la recherche, Association étudiante des cycles 
> supérieurs en psychologie de l'Université de Montréal (AÉCSPUM)
> Université de Montréal
> Centre de recherche de l'Institut universitaire de gériatrie de 
> Montréal, bureau M7819
>
>
> ___
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> 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] GLM error - cannot read fsgd file for reading

2017-08-09 Thread Nick Corriveau-Lecavalier

Hi Freesurfer team,


I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) with 0 
covariables at the moment, but I would like to add two eventually. I've been 
following the tutorial on this link: 
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write the 
command it says ''cannot open g3v0.fsgd for reading''.


In my /subjects/fsgd file, there is my fsgd file, and my contrast file. Am I 
missing an additionnal file or something? Is the format of my files correct?


If it can help, here's what my fsgd file looks likes:

GroupDescriptorFile 1
Title OSGM
Class Control
Class SCD
Class MCI
Variables
Input 3431566 CTL
Input 3514091 CTL
Input 4051959 CTL
Input 4344061 CTL
Input 4557550 CTL
Input 7060373 CTL
Input 7274924 CTL
Input 7308293 CTL
Input 7424803 CTL
Input 7459501 CTL
Input 7543023 CTL
Input 7661810 CTL
Input 8069157 CTL
Input 8330218 CTL
Input 8656527 CTL
Input 8875385 CTL
Input 9296157 CTL
Input 3025432 SCD
Input 3494204 SCD
Input 3702154 SCD
Input 3708747 SCD
Input 3865361 SCD
Input 4316663 SCD
Input 4509950 SCD
Input 4548020 SCD
Input 4893763 SCD
Input 5381177 SCD
Input 5477234 SCD
Input 5522727 SCD
Input 6121388 SCD
Input 6168985 SCD
Input 6258913 SCD
Input 6274286 SCD
Input 6334263 SCD
Input 6417837 SCD
Input 6427603 SCD
Input 7435733 SCD
Input 7485585 SCD
Input 7712552 SCD
Input 8827943 SCD
Input 8980899 SCD

Regards,


Nick Corriveau-Lecavalier, B.Sc. (Hons)
Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique
Coordonateur à la recherche, Association étudiante des cycles supérieurs en 
psychologie de l'Université de Montréal (AÉCSPUM)
Université de Montréal
Centre de recherche de l'Institut universitaire de gériatrie de Montréal, 
bureau M7819
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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Z Hessam

of course:

hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v
bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red
bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red

mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
-1): read error
MRIread failed: Unable to read from
/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
-1): read error
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
-1): read error
MRIread failed: Unable to read from
/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz,
-1): read error

thanks a lot for your attention

On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang 
wrote:

> Can you copy and paste the exact command line you ran and the error
> message?
>
> Ruopeng
>
>
> On 08/09/2017 02:21 PM, Z Hessam wrote:
>
>
> I try it without \ chars, works for some other subjects
> but it doesn't work for one of them,and now I can even open it with GUI,
> while I could open it before.
> It seems that is time variant!
> Should I run "recon-all ..." again for that subject?
>
>
>
>
> On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl 
> wrote:
>
>> can you try it without all the \ characters?  You shouldn't need them if
>> it's all on one line
>>
>> On Wed, 9 Aug 2017, Z Hessam wrote:
>>
>>
>>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
>>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> MRIread failed: Unable to read from
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>> mri_read(): couldn't determine type of file
>>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>>
>>>
>>> I use the example 4 in the "download and install" page of site
>>>
>>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl >> >
>>> wrote:
>>>
>>>   hmmm, that looks ok, but it's hard to tell with all the
>>>   backslashes and blank lines and such. Can you send the full
>>>   command on a single line (e.g. by hitting up-arrow in the
>>>   terminal window) and the actual output of freeview?
>>>
>>>On Wed, 9 Aug 2017, Z Hessam wrote:
>>>
>>>
>>> Hello Freesurfer Developers,
>>>
>>> I have problem when I use "freeview" example code in
>>> terminal,
>>> freeview -v \
>>>
>>> bert/mri/T1.mgz \
>>>
>>> bert/mri/wm.mgz \
>>>
>>> bert/mri/brainmask.mgz \
>>>
>>>
>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>>
>>> -f \
>>>
>>> bert/surf/lh.white:edgecolor=blue \
>>>
>>> bert/surf/lh.pial:edgecolor=red \
>>>
>>> bert/surf/rh.white:edgecolor=blue \
>>>
>>> bert/surf/rh.pial:edgecolor=red
>>> it tell "Failed to load MRI ",
>>> mri_read(): couldn't determine type of file
>>> 
>>> MRIread failed: Unable to read from 
>>> mri_read(): couldn't determine type of file
>>> 
>>> but i can load wm.mgz and other existed files in
>>> GUI.
>>>
>>> please help me to know why this error happend? and
>>> what should I do to solve
>>>  this?
>>>
>>> I've searched the list, I found a similar errors,
>>> but wasn't helpful answer reported.
>>> help me please
>>>
>>> regards
>>>
>>> On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
>>>  wrote:
>>>
>>> Hello Freesurfer Developers,
>>>
>>> I have problem when I use "freeview" example code in
>>> terminal,
>>> freeview
>>> -v \
>>>
>>> bert/mri/T1.mgz \
>>>
>>> bert/mri/wm.mgz \
>>>
>>> bert/mri/brainmask.mgz \
>>>
>>>
>>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>>
>>> -f \
>>>
>>> bert/surf/lh.white:edgecolor=blue \
>>>
>>> bert/surf/lh.pial:edgecolor=red \
>>>
>>> bert/surf/rh.white:edgecolor=blue \
>>>
>>> bert/surf/rh.pial:edgecolor=red
>>> it tell "Failed to load MRI ", but i
>>> can load wm.mgz and other existed files in GUI.
>>>
>>> please help me to know why this error happend? and
>>> what should I do to solve
>>>  this?
>>>
>>> I've searched

Re: [Freesurfer] Pial surface editing

2017-08-09 Thread Bruce Fischl

can you send us the output of mri_info on orig.mgz and brainmask.mgz 
created with the -rl flag? And also send us the full screen output of the 
command that fails?


thanks
Bruce
 On Wed, 9 Aug 2017, Michelle VanTieghem 
wrote:



Hi, 
I originally used 
mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz 

and I re-did it using  the -rl flag as you recommended. 

it did not influence anything, same problem. 

I'd appreciate any trouble shooting tips. 

Thanks,
M

On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl 
wrote:
  what was your mri_convert command line? It should be something
  like

  mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz

  cheers
  Bruce

  On Mon, 7 Aug 2017, Michelle VanTieghem wrote:

Hi Bruce, 

Here is what I did. For each subject:
a) used the original (non-skull stripped) brain for
the 001.mgz file as input -
located in the Subnum/mri directory
b) used mri_convert to get the afni skull-stripped
brains and renamed them
"brainmask.mgz" , located in the Subnum/mri
directory. 
c) Then I ran the following command:

recon-all -all -3T -mprage -s processed/Subnum


I get the following error:
 -- 
                         
                                   
#@# Mask BFS Sat Aug  5 01:31:09 EDT 2017
/vega/psych/users/mrv2115/fsdata/processed/SB002/mri

 mri_mask -T 5 brain.mgz brainmask.mgz
brain.finalsurfs.mgz

threshold mask volume at 5
ERROR: dimension mismatch between source and mask
-

Can you please advise?





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HelpLine at
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--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2...@columbia.edu

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Re: [Freesurfer] Pial surface editing

2017-08-09 Thread Michelle VanTieghem

Hi,

I originally used
mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz

and I re-did it using  the -rl flag as you recommended.

it did not influence anything, same problem.

I'd appreciate any trouble shooting tips.

Thanks,
M

On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl 
wrote:

> what was your mri_convert command line? It should be something like
>
> mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz
>
> cheers
> Bruce
>
>
> On Mon, 7 Aug 2017, Michelle VanTieghem wrote:
>
> Hi Bruce,
>>
>> Here is what I did. For each subject:
>> a) used the original (non-skull stripped) brain for the 001.mgz file as
>> input -
>> located in the Subnum/mri directory
>> b) used mri_convert to get the afni skull-stripped brains and renamed them
>> "brainmask.mgz" , located in the Subnum/mri directory.
>> c) Then I ran the following command:
>>
>> recon-all -all -3T -mprage -s processed/Subnum
>>
>>
>> I get the following error:
>>  --
>>
>>
>> #@# Mask BFS Sat Aug  5 01:31:09 EDT 2017
>> /vega/psych/users/mrv2115/fsdata/processed/SB002/mri
>>
>>  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
>>
>> threshold mask volume at 5
>> ERROR: dimension mismatch between source and mask
>> -
>>
>> Can you please advise?
>>
>>
>>
>>
>
> 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.
>



-- 
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu
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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Ruopeng Wang

Can you copy and paste the exact command line you ran and the error message?

Ruopeng

On 08/09/2017 02:21 PM, Z Hessam wrote:

I try it without \ chars, works for some other subjects
but it doesn't work for one of them,and now I can even open it with 
GUI, while I could open it before.

It seems that is time variant!
Should I run "recon-all ..." again for that subject?

On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl 
> wrote:

can you try it without all the \ characters?  You shouldn't need
them if it's all on one line

On Wed, 9 Aug 2017, Z Hessam wrote:

$>freeview -v \bert/mri/T1.mgz \ bert/mri/wm.mgz \
bert/mri/brainmask.mgz \
bert/mri/aseg.mgz:colormap=lut:opacity=0.2
mri_read(): couldn't determine type of file
/media/hessam91/driver2/freesurfer/freesurfer/subjects/
MRIread failed: Unable to read from
/media/hessam91/driver2/freesurfer/freesurfer/subjects/
mri_read(): couldn't determine type of file
/media/hessam91/driver2/freesurfer/freesurfer/subjects/

I use the example 4 in the "download and install" page of site

On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl
>
wrote:

  hmmm, that looks ok, but it's hard to tell with all the
  backslashes and blank lines and such. Can you send the full
  command on a single line (e.g. by hitting up-arrow in the
  terminal window) and the actual output of freeview?

   On Wed, 9 Aug 2017, Z Hessam wrote:

Hello Freesurfer Developers,

I have problem when I use "freeview" example code in
terminal,
freeview -v \

bert/mri/T1.mgz \

bert/mri/wm.mgz \

bert/mri/brainmask.mgz \

bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

-f \

bert/surf/lh.white:edgecolor=blue \

bert/surf/lh.pial:edgecolor=red \

bert/surf/rh.white:edgecolor=blue \

bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI ",
mri_read(): couldn't determine type of file

MRIread failed: Unable to read from 
mri_read(): couldn't determine type of file

but i can load wm.mgz and other existed files in
GUI.

please help me to know why this error happend? and
what should I do to solve
 this?

I've searched the list, I found a similar errors,
but wasn't helpful answer reported.
help me please

regards

On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
>
wrote:

Hello Freesurfer Developers,

I have problem when I use "freeview" example code in
terminal,
freeview
-v \

bert/mri/T1.mgz \

bert/mri/wm.mgz \

bert/mri/brainmask.mgz \

bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

-f \

bert/surf/lh.white:edgecolor=blue \

bert/surf/lh.pial:edgecolor=red \

bert/surf/rh.white:edgecolor=blue \

bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI ", but i
can load wm.mgz and other existed files in GUI.

please help me to know why this error happend? and
what should I do to solve
 this?

I've searched the list, I found a similar errors,
but wasn't helpful answer reported.
help me please

regards

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HelpLine at

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Z Hessam

I try it without \ chars, works for some other subjects
but it doesn't work for one of them,and now I can even open it with GUI,
while I could open it before.
It seems that is time variant!
Should I run "recon-all ..." again for that subject?




On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl 
wrote:

> can you try it without all the \ characters?  You shouldn't need them if
> it's all on one line
>
> On Wed, 9 Aug 2017, Z Hessam wrote:
>
>
>> $>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
>> bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> MRIread failed: Unable to read from
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>> mri_read(): couldn't determine type of file
>> /media/hessam91/driver2/freesurfer/freesurfer/subjects/
>>
>>
>> I use the example 4 in the "download and install" page of site
>>
>> On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl 
>> wrote:
>>
>>   hmmm, that looks ok, but it's hard to tell with all the
>>   backslashes and blank lines and such. Can you send the full
>>   command on a single line (e.g. by hitting up-arrow in the
>>   terminal window) and the actual output of freeview?
>>
>>On Wed, 9 Aug 2017, Z Hessam wrote:
>>
>>
>> Hello Freesurfer Developers,
>>
>> I have problem when I use "freeview" example code in
>> terminal,
>> freeview -v \
>>
>> bert/mri/T1.mgz \
>>
>> bert/mri/wm.mgz \
>>
>> bert/mri/brainmask.mgz \
>>
>>
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>
>> -f \
>>
>> bert/surf/lh.white:edgecolor=blue \
>>
>> bert/surf/lh.pial:edgecolor=red \
>>
>> bert/surf/rh.white:edgecolor=blue \
>>
>> bert/surf/rh.pial:edgecolor=red
>> it tell "Failed to load MRI ",
>> mri_read(): couldn't determine type of file
>> 
>> MRIread failed: Unable to read from 
>> mri_read(): couldn't determine type of file
>> 
>> but i can load wm.mgz and other existed files in
>> GUI.
>>
>> please help me to know why this error happend? and
>> what should I do to solve
>>  this?
>>
>> I've searched the list, I found a similar errors,
>> but wasn't helpful answer reported.
>> help me please
>>
>> regards
>>
>> On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
>>  wrote:
>>
>> Hello Freesurfer Developers,
>>
>> I have problem when I use "freeview" example code in
>> terminal,
>> freeview
>> -v \
>>
>> bert/mri/T1.mgz \
>>
>> bert/mri/wm.mgz \
>>
>> bert/mri/brainmask.mgz \
>>
>>
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>
>> -f \
>>
>> bert/surf/lh.white:edgecolor=blue \
>>
>> bert/surf/lh.pial:edgecolor=red \
>>
>> bert/surf/rh.white:edgecolor=blue \
>>
>> bert/surf/rh.pial:edgecolor=red
>> it tell "Failed to load MRI ", but i
>> can load wm.mgz and other existed files in GUI.
>>
>> please help me to know why this error happend? and
>> what should I do to solve
>>  this?
>>
>> I've searched the list, I found a similar errors,
>> but wasn't helpful answer reported.
>> help me please
>>
>> regards
>>
>>
>>
>>
>> ___
>> 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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>
>
> 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

Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

2017-08-09 Thread Bruce Fischl

they probably aren't from the right dicom series then.
On Wed, 9 Aug 2017, 
Yagmur Ozdemir 19 wrote:

> I tried that and realized the images are very blurry so it probably will not 
> run in any case.
>
> Thank you!
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, August 09, 2017 1:20 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] multi-frame input error with PAR/SEC origin file
>
> Hi Idil
> you have to figure out what the input volume has more than 1 frame (that
> is, why is it 4d). It could be because you saved phase and mag, or because
> there are multiple echoes, but until you understand what the additional
> frames are we can't process it. YOu can start by bringing the orig.mgz up
> in freeview and looking at it and seeing what the different frames look
> like. If one of them looks like the T1-weighted image and the other doesn't
> (maybe it's a phase map?) you would run:
>
> cd  /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/
> mv 001.mgz 001.multiframe.mgz
> mri_convert -nth 0 001.multiframe.mgz 001.mgz
>
>
> assuming that the 0th (first) frame is the T1 weighted. If it was the next
> one you would do -nth 1 instead
>
> cheers
> Bruce
>
>
> On Tue, 8 Aug 2017, Yagmur Ozdemir 19 wrote:
>
>> Hello FreeSurfer experts,
>>
>> I am trying to run recon-all on a nifti file converted from PAR/SEC using
>> dcm2niix, and this error came up pretty soon after the script started to
>> run;
>>
 mri_convert.bin
>> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz
>> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>> reading from
>> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (-0, 0.916013, -0.401149)
>> k_ras = (0, 0.401149, 0.916013)
>> writing to
>> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz...
>> #
>> #@# MotionCor Tue Aug  8 17:42:13 EDT 2017
>> Found 1 runs
>> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
>> Checking for (invalid) multi-frame inputs...
>> ERROR: input(s) cannot have multiple frames!
>>
>> I am pretty inexperienced with FreeSurfer, but does this error mean I need
>> to slice my file? I would really appreciate if someone could give me some
>> ideas for commands to use.
>>
>> Thank you all!
>> Best,
>> Idil
>>
>>
>>
>>
>
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> Freesurfer mailing list
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>
>
>
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Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

2017-08-09 Thread Yagmur Ozdemir 19

I tried that and realized the images are very blurry so it probably will not 
run in any case. 

Thank you!
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, August 09, 2017 1:20 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

Hi Idil
you have to figure out what the input volume has more than 1 frame (that
is, why is it 4d). It could be because you saved phase and mag, or because
there are multiple echoes, but until you understand what the additional
frames are we can't process it. YOu can start by bringing the orig.mgz up
in freeview and looking at it and seeing what the different frames look
like. If one of them looks like the T1-weighted image and the other doesn't
(maybe it's a phase map?) you would run:

cd  /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/
mv 001.mgz 001.multiframe.mgz
mri_convert -nth 0 001.multiframe.mgz 001.mgz

assuming that the 0th (first) frame is the T1 weighted. If it was the next
one you would do -nth 1 instead

cheers
Bruce

On Tue, 8 Aug 2017, Yagmur Ozdemir 19 wrote:

> Hello FreeSurfer experts,
>
> I am trying to run recon-all on a nifti file converted from PAR/SEC using
> dcm2niix, and this error came up pretty soon after the script started to
> run;
>
> >> mri_convert.bin
> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz
> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from
> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (-0, 0.916013, -0.401149)
> k_ras = (0, 0.401149, 0.916013)
> writing to
> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz...
> #
> #@# MotionCor Tue Aug  8 17:42:13 EDT 2017
> Found 1 runs
> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> ERROR: input(s) cannot have multiple frames!
>
> I am pretty inexperienced with FreeSurfer, but does this error mean I need
> to slice my file? I would really appreciate if someone could give me some
> ideas for commands to use.
>
> Thank you all!
> Best,
> Idil
>
>
>
>

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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Bruce Fischl

can you try it without all the \ characters?  You shouldn't need them if 
it's all on one line

On Wed, 9 Aug 2017, Z Hessam wrote:



$>freeview -v \    bert/mri/T1.mgz \    bert/mri/wm.mgz \   
bert/mri/brainmask.mgz \    bert/mri/aseg.mgz:colormap=lut:opacity=0.2
mri_read(): couldn't determine type of file
/media/hessam91/driver2/freesurfer/freesurfer/subjects/
MRIread failed: Unable to read from
/media/hessam91/driver2/freesurfer/freesurfer/subjects/
mri_read(): couldn't determine type of file
/media/hessam91/driver2/freesurfer/freesurfer/subjects/


I use the example 4 in the "download and install" page of site

On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl 
wrote:

  hmmm, that looks ok, but it's hard to tell with all the
  backslashes and blank lines and such. Can you send the full
  command on a single line (e.g. by hitting up-arrow in the
  terminal window) and the actual output of freeview?

   On Wed, 9 Aug 2017, Z Hessam wrote:


Hello Freesurfer Developers,

I have problem when I use "freeview" example code in
terminal,
freeview -v \

    bert/mri/T1.mgz \

    bert/mri/wm.mgz \

    bert/mri/brainmask.mgz \

   
    bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

    -f \

    bert/surf/lh.white:edgecolor=blue \

    bert/surf/lh.pial:edgecolor=red \

    bert/surf/rh.white:edgecolor=blue \

    bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI ",
mri_read(): couldn't determine type of file

MRIread failed: Unable to read from 
mri_read(): couldn't determine type of file

but i can load wm.mgz and other existed files in
GUI.

please help me to know why this error happend? and
what should I do to solve
 this?

I've searched the list, I found a similar errors,
but wasn't helpful answer reported.
help me please

regards

On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam
 wrote:

Hello Freesurfer Developers,

I have problem when I use "freeview" example code in
terminal,
freeview
-v \

    bert/mri/T1.mgz \

    bert/mri/wm.mgz \

    bert/mri/brainmask.mgz \

   
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

    -f \

    bert/surf/lh.white:edgecolor=blue \

    bert/surf/lh.pial:edgecolor=red \

    bert/surf/rh.white:edgecolor=blue \

    bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI ", but i
can load wm.mgz and other existed files in GUI.

please help me to know why this error happend? and
what should I do to solve
 this?

I've searched the list, I found a similar errors,
but wasn't helpful answer reported.
help me please

regards




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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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and properly
dispose of the e-mail.



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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Z Hessam

$>freeview -v \bert/mri/T1.mgz \bert/mri/wm.mgz \
bert/mri/brainmask.mgz \bert/mri/aseg.mgz:colormap=lut:opacity=0.2
mri_read(): couldn't determine type of file
/media/hessam91/driver2/freesurfer/freesurfer/subjects/
MRIread failed: Unable to read from
/media/hessam91/driver2/freesurfer/freesurfer/subjects/
mri_read(): couldn't determine type of file
/media/hessam91/driver2/freesurfer/freesurfer/subjects/


I use the example 4 in the "download and install" page of site

On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl 
wrote:

>
> hmmm, that looks ok, but it's hard to tell with all the backslashes and
> blank lines and such. Can you send the full command on a single line (e.g.
> by hitting up-arrow in the terminal window) and the actual output of
> freeview?
>
>
>  On Wed, 9 Aug 2017, Z Hessam wrote:
>
>
>> Hello Freesurfer Developers,
>>
>> I have problem when I use "freeview" example code in terminal,
>> freeview -v \
>>
>> bert/mri/T1.mgz \
>>
>> bert/mri/wm.mgz \
>>
>> bert/mri/brainmask.mgz \
>>
>>
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>
>> -f \
>>
>> bert/surf/lh.white:edgecolor=blue \
>>
>> bert/surf/lh.pial:edgecolor=red \
>>
>> bert/surf/rh.white:edgecolor=blue \
>>
>> bert/surf/rh.pial:edgecolor=red
>> it tell "Failed to load MRI ",
>> mri_read(): couldn't determine type of file 
>> MRIread failed: Unable to read from  mri_read(): couldn't
>> determine type of file 
>> but i can load wm.mgz and other existed files in GUI.
>>
>> please help me to know why this error happend? and what should I do to
>> solve
>>  this?
>>
>> I've searched the list, I found a similar errors, but wasn't helpful
>> answer reported.
>> help me please
>>
>> regards
>>
>> On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam  wrote:
>>
>> Hello Freesurfer Developers,
>>
>> I have problem when I use "freeview" example code in terminal,
>> freeview
>> -v \
>>
>> bert/mri/T1.mgz \
>>
>> bert/mri/wm.mgz \
>>
>> bert/mri/brainmask.mgz \
>>
>>
>> bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
>>
>> -f \
>>
>> bert/surf/lh.white:edgecolor=blue \
>>
>> bert/surf/lh.pial:edgecolor=red \
>>
>> bert/surf/rh.white:edgecolor=blue \
>>
>> bert/surf/rh.pial:edgecolor=red
>> it tell "Failed to load MRI ", but i can load wm.mgz and
>> other existed files in GUI.
>>
>> please help me to know why this error happend? and what should I do to
>> solve
>>  this?
>>
>> I've searched the list, I found a similar errors, but wasn't helpful
>> answer reported.
>> help me please
>>
>> regards
>>
>>
>>
>>
> ___
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> 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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Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Bruce Fischl



hmmm, that looks ok, but it's hard to tell with all the backslashes and 
blank lines and such. Can you send the full command on a single line (e.g. 
by hitting up-arrow in the terminal window) and the actual output of 
freeview?


 On Wed, 9 Aug 2017, Z Hessam 
wrote:




Hello Freesurfer Developers,

I have problem when I use "freeview" example code in terminal,
freeview -v \

    bert/mri/T1.mgz \

    bert/mri/wm.mgz \

    bert/mri/brainmask.mgz \

   
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

    -f \

    bert/surf/lh.white:edgecolor=blue \

    bert/surf/lh.pial:edgecolor=red \

    bert/surf/rh.white:edgecolor=blue \

    bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI ",
mri_read(): couldn't determine type of file 
MRIread failed: Unable to read from  
mri_read(): couldn't determine type of file 

but i can load wm.mgz and other existed files in GUI.

please help me to know why this error happend? and what should I do to solve
 this?

I've searched the list, I found a similar errors, but wasn't helpful answer 
reported.

help me please

regards

On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam  wrote:

Hello Freesurfer Developers,

I have problem when I use "freeview" example code in terminal,
freeview
-v \

    bert/mri/T1.mgz \

    bert/mri/wm.mgz \

    bert/mri/brainmask.mgz \

   
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \

    -f \

    bert/surf/lh.white:edgecolor=blue \

    bert/surf/lh.pial:edgecolor=red \

    bert/surf/rh.white:edgecolor=blue \

    bert/surf/rh.pial:edgecolor=red
it tell "Failed to load MRI ", but i can load wm.mgz and other 
existed files in GUI.


please help me to know why this error happend? and what should I do to solve
 this?

I've searched the list, I found a similar errors, but wasn't helpful answer 
reported.

help me please

regards



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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Z Hessam

Hello Freesurfer Developers,

I have problem when I use "freeview" example code in terminal,

freeview -v \
bert/mri/T1.mgz \
bert/mri/wm.mgz \
bert/mri/brainmask.mgz \
   bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f \
bert/surf/lh.white:edgecolor=blue \
bert/surf/lh.pial:edgecolor=red \
bert/surf/rh.white:edgecolor=blue \
bert/surf/rh.pial:edgecolor=red

it tell "Failed to load MRI ",

mri_read(): couldn't determine type of file 
MRIread failed: Unable to read from 
mri_read(): couldn't determine type of file 

but i can load wm.mgz and other existed files in GUI.

please help me to know why this error happend? and what should I do to
solve this?

I've searched the list, I found a similar errors, but wasn't helpful
answer reported.
help me please

regards

On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam  wrote:

> Hello Freesurfer Developers,
>
> I have problem when I use "freeview" example code in terminal,
>
> freeview
> -v \
> bert/mri/T1.mgz \
> bert/mri/wm.mgz \
> bert/mri/brainmask.mgz \
>bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
> -f \
> bert/surf/lh.white:edgecolor=blue \
> bert/surf/lh.pial:edgecolor=red \
> bert/surf/rh.white:edgecolor=blue \
> bert/surf/rh.pial:edgecolor=red
>
> it tell "Failed to load MRI ", but i can load wm.mgz and other 
> existed files in GUI.
>
> please help me to know why this error happend? and what should I do to solve 
> this?
>
> I've searched the list, I found a similar errors, but wasn't helpful answer 
> reported.
> help me please
>
> regards
>
>
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] "failed to load mri" in terminal, not in GUI

2017-08-09 Thread Z Hessam

Hello Freesurfer Developers,

I have problem when I use "freeview" example code in terminal,

freeview
-v \
bert/mri/T1.mgz \
bert/mri/wm.mgz \
bert/mri/brainmask.mgz \
   bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f \
bert/surf/lh.white:edgecolor=blue \
bert/surf/lh.pial:edgecolor=red \
bert/surf/rh.white:edgecolor=blue \
bert/surf/rh.pial:edgecolor=red

it tell "Failed to load MRI ", but i can load wm.mgz and
other existed files in GUI.

please help me to know why this error happend? and what should I do to
solve this?

I've searched the list, I found a similar errors, but wasn't helpful
answer reported.
help me please

regards
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Gcuts erasing voxels within the ventricles

2017-08-09 Thread Bruce Fischl


Hi Elijah

gcuts is a contributed tool (from Mike Chee's lab) and not one that we 
wrote, so I don't think we can help.


sorry
Bruce
On Wed, 9 Aug 2017, 
Elijah Mak wrote:



Hi Freesurfer Team,

I am using gcut to improve the skull stripping on some subjects. I noticed
that it is also removing some of the voxels in the ventricles of the
brainmask.mgz (picture attached). Is this normal behaviour? 

Thanks for your time.

Best Wishes,
Elijah 



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[Freesurfer] RA/programmer job posting - neuroinformatics, big data {Disarmed} {Disarmed}

2017-08-09 Thread Gregory Book

The Olin Neuropsychiatry Research Center (http://nrc-iol.org
)
located in Hartford, CT USA is looking for a research assistant II/data
manager (or post-doc, depending on candidate) to assist with data
management, neuroinformatics development, and big-data analyses. The Olin
Center is a 40 person department, opened in 2003 at the Institute of
Living. We have a Siemens Skyra 3T whole-body MRI, EEG, and TMS suites. The
Olin Center's database of 30,000 imaging sessions also provides an
internally accessible source of data for the candidate's own analyses, and
a 350 node compute cluster with 0.5PB storage is available to use. We are
looking for an RA or post-doc to help develop the Neuroinformatics Database
(http://github.com/gbook/nidb

), manage neuroimaging data, and assist with the programming of automated
neuroimaging processing systems. The primary focus and approximately half
of the position will be developing and maintaining imaging and non-imaging
databases, but duties will also include responding to support requests,
training, documentation, and bug fixing. The other half of the position
will be analyzing data and contributing to manuscripts. Candidate is
expected to have a bachelor’s degree (PhD for post-doc) and experience with
at least 1 programming language. Attention to detail and database
experience are very desirable. Experience programming PHP, Perl, HTML, SQL,
in a Linux environment is strongly preferred. Neuroimaging experience is
also preferred, but not necessary. Contact Greg at
gregory.b...@hhchealth.org

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[Freesurfer] Research Assistant Position at The Ohio State University

2017-08-09 Thread Herring, Elizabeth J.

Research Assistant Position

Clinical Neuroscience Laboratory
Department of Psychology
Ohio State University

Applications are being sought for a full-time research assistant position, 
starting autumn semester 2017 in the Clinical Neuroscience 
Laboratory of Dr. Ruchika 
Prakash at the Ohio State University. The laboratory is currently conducting 
several randomized controlled trials designed to look at the effects of 
lifestyle interventions, such as mindfulness training and exercise 
interventions on improving cognitive and emotional control in older adults and 
in individuals with multiple sclerosis. This position is designed for 
individuals with existing research experience who are interested in gaining 
knowledge in the new field of health neuroscience. Experience with programming 
and neuroimaging data analysis with FSL, AFNI, or SPM is strongly preferred. 
Responsibilities will include active involvement in all aspects of research, 
facilitating recruitment efforts between the laboratory and community partners, 
and overseeing day-to-day operations of the laboratory.

If you are interested in being considered for the position, please apply online 
at https://www.jobsatosu.com,under job listing #430999 and submit a current CV, 
a brief statement of interest, and names of three references.,

If you have questions about the position or the lab, please contact Dr. Ruchika 
Prakash at prakash...@osu.edu

Lab Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html

The Ohio State University is an equal opportunity employer. All qualified 
applicants will receive consideration for employment without regard to race, 
color, religion, sex, sexual orientation or identity, national origin, 
disability status, or protected veteran status.
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[Freesurfer] PhD Scholarship at Aston Brain Centre (UK)

2017-08-09 Thread King, Daniel (Research Student)

Dear Mailing List,

Feel free to distribute the advertisement below for a PhD scholarship on an 
exciting machine learning project as you see fit.

Best wishes,

Daniel King

PhD Candidate in Neurosciences,
School of Life and Health Sciences & Aston Brain Centre (SW505),
Aston University,
Aston Triangle, B4 7ET
West Midlands, UK


Email: kin...@aston.ac.uk
Twitter: @danieljking8




PhD Studentship - Computational modelling of brain images with lesions and 
their application to machine learning approaches to predicting child outcomes
Life and Health Sciences - Studentships
Contract Type:

Fixed Term (for 3 years)

Basis:

Full Time

Closing Date:

23.59 hours BST on Thursday 24 August 2017

Reference:

R170352


Supervisors: Professor Amanda Wood, Dr Jan Novak & Dr Elaine Foley

Applications  are  invited  from  highly  motivated  candidates  for  a  
project  that  will  use  advanced magnetic resonance imaging (MRI) methods to 
investigate traumatic brain injury in children. This opportunity is open to UK 
and EU students who have at least an Upper Second Class Honours degree (2.1) or 
equivalent in Computational or Physical sciences.

The study will involve assessment of more than 800 children recruited in 
Birmingham and the overall study will examine Neuroimaging and Neurobehavioural 
data in nearly 1000 children.  Analysis of the multimodal dataset will allow 
the construction of a model which will predict patient outcome after a 
traumatic brain injury allowing stratification of treatment and mitigate 
deficit.

The successful candidate will join a multidisciplinary team who combine 
neurocognitive assessment with advanced image acquisition and analysis. It is 
expected that the candidate will have experience in computer programming using 
languages such as Matlab and/or Python and have some experience of image 
analysis and matrix manipulation.

Aston University was ranked   5th  out of 94 UK Higher Education Institutions 
for research in Allied Health Professions (REF 2014) and was ranked 1st for 
research environment.  Additional information about  research  in  the  School  
can  be  found  at   http://www.aston.ac.uk/lhs/research/.Informal 
enquiries can be made to Professor Amanda Wood 
(a.wo...@aston.ac.uk) or Dr Jan Novak 
(j.no...@aston.ac.uk).

Financial Support:

The studentship is open to Home/EU students only and comprises of a tax-free 
stipend at the
2017/18 RCUK rate of £14,553 p.a. and payment of Home/EU tuition fees only. The 
studentship is available for three years, subject to satisfactory progress 
review at the end of the first year, with an anticipated registration date of 
1st October 2017.

Application Requirements:

Eligible Applicants should hold at least a Bachelor (Hons.) Degree of either 
1st  Class/ 2.1 or MSc/MRes in Computer Science, Engineering, Mathematics, 
Statistics or Physics.

EU Applicants will need to demonstrate adequate proficiency in English Language 
skills, with a minimum overall score of 93 (Internet Based) (with a minimum 
score in each section of: R: 18, W: 23, L: 19 and S: 19) in TOEFL or IELTS with 
minimum marks of 6.0 in each section and an overall band of 6.5.

Informal  enquiries  should  be  addressed  to  Professor  Amanda  Wood  
(E-mail: a.wo...@aston.ac.uk; Telephone: +44 (0) 
121 204 3593) or Dr Jan Novak (E-mail: 
j.no...@aston.ac.uk; Telephone: +44 (0) 121 (0) 204 
3079).

To apply please complete the  on-line application form at 
http://www1.aston.ac.uk/lhs/research/postgraduate-research/apply/, choosing 
'Research Full-Time Health Sciences September 2017' quoting the Reference: 
'PhD_Wood PROBIt-1' on all applications.

The Closing Date for all Applications is: Thursday 24th August 2017.

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Re: [Freesurfer] Total White matter and CSF value Calculation

2017-08-09 Thread M Janani

Thanks Douglas

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: 02 August 2017 21:15
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Total White matter and CSF value Calculation

The first formula is right. I would not trust the 2nd formula since we don't 
compute actual ICV

On 8/2/17 2:22 AM, M Janani wrote:

Hi Douglas,

Thanks for your support.

From the below conclusion, can I say

Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + 
rh)Inf-Lat-Vent + (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle + 5th 
Ventricle + CSF.

Also Is it correct to compute Total CSF using the below mentioned 
formula

Total CSF = Intracranial Volume - (Total white matter + Total Gray 
matter)

Regards,

Janani

Douglas 
Greve
 Mon, 31 Jul 2017 07:48:02 
-0700

On 7/31/17 3:12 AM, M Janani wrote:

Hi Team,

Could you please confirm whether the below mentioned formulas to compute Total 
WM and ventricular CSF are correct

1.Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum White Matter

looks right, though some times people will include brainstem as part of WM

2.Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent 
+ (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle

There is a 5th ventricle (which I think is basically the aqueduct). There is 
also a segment called "CSF" (24) but can't remember what gets labeled as "CSF"

Thanks for your support.

Regards,

Janani

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[Freesurfer] Gcuts erasing voxels within the ventricles

2017-08-09 Thread Elijah Mak

Hi Freesurfer Team,

I am using gcut to improve the skull stripping on some subjects. I noticed that 
it is also removing some of the voxels in the ventricles of the brainmask.mgz 
(picture attached). Is this normal behaviour? 

Thanks for your time.

Best Wishes,
Elijah 


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[Freesurfer] convert mgh to nii problems - cannot get output file to reshape properly

2017-08-09 Thread Suzanne Witt

Hi.

I am having a problem similar to that previously described on the freesurfer 
message boards from May 2011 (Subject: mgh conversion).  Unfortunately, that 
thread ends with Doug asking the person to send him the files in question, so 
there does not appear to be any sort of publicly published solution.  

I was sent two .mgh files with the resulting activation maps from an fMRI 
analysis (both left and right hemispheres) and told that the maps were in 
fsaverage space.  I was not sent any other accompanying files.  I am trying to 
convert them to nii format.

I have tried both:
 
1. mri_convert filename.mgh filename.nii.gz 

and mri_surf2surf (as was suggested in the previous thread)

2. mri_surf2surf —sval filename.mgh —tval filename.nii —reshape —reshape-factor 
6 —s fsaverage —hemi lh

(I realize that the command options should be preceded by double dashes, but my 
email program is quite insistent about automatically formatting these to long 
dashes.)

In both cases the when checking the output file using mri_info, the dimensions 
are still: 163842 x 1 x 1.

Are there any suggestions as to how best to proceed?  

Thanks in advance,

Suzanne Witt

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[Freesurfer] Freesurfer 6.0 and 5.3 differences in eTIV but not in supratentorial volume

2017-08-09 Thread Lucette Cysique

Hello all


FYI

I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my 
healthy young sample

It is probably due to the cerebellum computation changes (presented in released 
notes for 6.0)

Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar

(all was checked by simple correlations)


Could people who have good knowledge of cerebellum studies  comment on the 
reliability of freesurfer 5.3 in assessing size of the cerebellum versus manual 
tracing? This may need to be redone for version 6.0.


Regards

Lucette



Lucette A. Cysique, Ph.D.

NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017
NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA
Senior Lecturer SoMs, UNSW Medicine
Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied 
Medical Research Centre, Peter Duncan Neuroscience Unit

Postal Address:
Neuroscience Research Australia
PO Box 1165 (Street Address: 139 Barker Street)
Randwick NSW 2031
Australia

Office Ph: +61 2 9399 1880
Mobile Ph: (+61)  (0)431 576 710 (text preferred)

Emails:
lcysi...@unsw.edu.au (primary)
lucette.cysi...@svha.org.au (St. Vincent's Hospital Sydney, related project)
lcysi...@ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project)
Twitter: @Lucette_C
http://www.neura.edu.au/research/themes/cysique-group
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[Freesurfer] Freesurfer PIB PET image processing

2017-08-09 Thread M Janani

Hi Team,

I apologize, I am new to Freesurfer .

Currently we are processing PIB PET images.

When we compare the SPM data along with FREESURFER outputs. We 
were able to see a large variation in the values.

Could you please guide us in processing PIB PET images in 
Freesurfer?

Since the signal of a PET image is very weak, we used MRI image 
as a guide to map it to Standard brain.

How does Freesurfer process in this case?

Your help would be grateful.

Regards,
Janani




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