Re: [Freesurfer] Freesurfer version from recon-all output files

[Diogo Duarte]

Thank you for your answer!

For future reference, info about the machine can be found in the
scripts/recon-all.done.

Diogo

On 25 April 2017 at 22:24, Douglas Greve  wrote:

> There is a file called scripts/build-stamp.txt. Also, if you set
> setenv REQUIRE_FS_MATCH 1
>
> It will compare the current version with the version in the build stamp
> and exit with error if they don't agree
>
>
> On 4/25/17 5:14 PM, Diogo Duarte wrote:
>
> Hi everyone,
>
> How can I find the freesurfer version used (recon-all) from the resulting
> files?
> This would be necessary for keeping freesurfer versions consistent.
>
> Thank you,
> Diogo
>
>
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> HelpLine at
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Re: [Freesurfer] Freesurfer version from recon-all output files

[Douglas Greve]

There is a file called scripts/build-stamp.txt. Also, if you set

setenv REQUIRE_FS_MATCH 1

It will compare the current version with the version in the build stamp 
and exit with error if they don't agree


On 4/25/17 5:14 PM, Diogo Duarte wrote:

Hi everyone,

How can I find the freesurfer version used (recon-all) from the 
resulting files?

This would be necessary for keeping freesurfer versions consistent.

Thank you,
Diogo


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[Freesurfer] Freesurfer version from recon-all output files

[Diogo Duarte]

Hi everyone,

How can I find the freesurfer version used (recon-all) from the resulting
files?
This would be necessary for keeping freesurfer versions consistent.

Thank you,
Diogo
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Re: [Freesurfer] FS 6.0 Freeview

[Z K]

As it currently stands, freeview can only be called via the terminal 
window by typing the 'freeview' at the command line. Creating a Desktop 
short cut will not work properly. We hope to support this feature in the 
near future.

-Zeke

On 04/25/2017 04:22 PM, 吕元媛 wrote:
> Dear Experts,
>
> I have the same problem with Freeview. I recently installed FS 6.0 on
> macOS Sierra (16E195).
> I have ran the command  “sudo -E fs_update” in terminal.
>
> When I start with Freeview app, load a volume, it will immediately
> crash. I attach the  problem report in the end.
>
> The only way to run freeview is from the terminal, but I cannot use the
> shortcuts with the Option (Alt) key, but other ones with Ctrl and
> Command functions well. I also have a warning message from the terminal
> window when I load a volume in this way.
> Freeview[694:13734] modalSession has been exited prematurely - check for
> a reentrant call to endModalSession:
>
> I tried to reinstall the OS but it didn’t work.
>
> Best, Yuanyuan
>
> -
> Process:   Freeview [1050]
> Path:
>  /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview
> Identifier:com.yourcompany.Freeview
> Version:   ???
> Code Type: X86-64 (Native)
> Parent Process:??? [1]
> Responsible:   Freeview [1050]
> User ID:   501
>
> Date/Time: 2017-04-25 22:01:12.682 +0200
> OS Version:Mac OS X 10.12.4 (16E195)
> Report Version:12
> Anonymous UUID:A853EAA1-CE03-1F51-19F0-A51C358DA386
>
>
> Time Awake Since Boot: 2100 seconds
>
> System Integrity Protection: enabled
>
> Crashed Thread:7
>
> Exception Type:EXC_CRASH (SIGABRT)
> Exception Codes:   0x, 0x
> Exception Note:EXC_CORPSE_NOTIFY
>
> Termination Reason:DYLD, [0x4] Symbol missing
>
> Dyld Error Message:
>   Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> Thread 0:: Dispatch queue: com.apple.main-thread
> 0   com.apple.CoreGraphics0x7fffd60c376c argb32_mark + 13240
> 1   com.apple.CoreGraphics0x7fffd60c6862 argb32_image + 1954
> 2   com.apple.CoreGraphics0x7fffd6490486 RIPLayerBltImage + 1039
> 3   com.apple.CoreGraphics0x7fffd61309da ripc_RenderImage + 228
> 4   com.apple.CoreGraphics0x7fffd6136199 ripc_EndLayer + 1411
> 5   com.apple.CoreGraphics0x7fffd6481bf5
> CGContextEndTransparencyLayer + 53
> 6   com.apple.coreui  0x7fffe1983dcb
> -[CUITextEffectStack
> drawGlyphs:inContext:usingFont:atPositions:count:lineHeight:inBounds:atScale:]
> + 1833
> 7   com.apple.coreui  0x7fffe195dfd4
> CUIRenderer::DrawStyledGlyphsAtPositions(CGContext*, __CFDictionary
> const*, __CTFont const*, unsigned short const*, CGPoint const*, unsigned
> long, double) + 2188
> 8   com.apple.coreui  0x7fffe195fbfe
> CUIDrawStyledGlyphsAtPositions + 275
> 9   com.apple.HIToolbox   0x7fffd51fa204
> _HIThemeCUIDrawStyledGlyphsAtPositions + 88
> 10  com.apple.HIToolbox   0x7fffd51f998c
> TCoreTextEngine::DrawThemeTextBox(THIThemeTextInfo*, CGRect const&,
> unsigned int, CGContext*) + 2220
> 11  com.apple.HIToolbox   0x7fffd51f9014
> ___ZN10DataEngine11DrawTextBoxEPKvPK6CGRectP15HIThemeTextInfoP9CGContext_block_invoke
> + 262
> 12  com.apple.HIToolbox   0x7fffd51f8ce8
> DataEngine::DrawTextBox(void const*, CGRect const*, HIThemeTextInfo*,
> CGContext*) + 1412
> 13  com.apple.HIToolbox   0x7fffd51f874c HIThemeDrawTextBox
> + 490
> 14  com.apple.HIToolbox   0x7fffd51f7d21
> HIMenuBarView::DrawTextTitle(MenuData*, CGRect const*, __CFString
> const*, unsigned short, CGContext*, bool, bool) + 379
> 15  com.apple.HIToolbox   0x7fffd51f317b
> HIMenuBarView::DrawOnce(CGRect, CGRect, bool, bool, CGContext*) + 1599
> 16  com.apple.HIToolbox   0x7fffd51f2a44
> HIMenuBarView::DrawSelf(short, __HIShape const*, CGContext*) + 554
> 17  com.apple.HIToolbox   0x7fffd51f246c
> HIMenuBarView::DrawWithoutCustomization(short, __HIShape const*,
> CGContext*) + 82
> 18  com.apple.HIToolbox   0x7fffd51f240b
> HIMenuBarView::DrawingDelegateHandler(OpaqueEventHandlerCallRef*,
> OpaqueEventRef*, void*) + 249
> 19  com.apple.HIToolbox   0x7fffd51d5d85
> DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*,
> HandlerCallRec*) + 1708
> 20  com.apple.HIToolbox   0x7fffd51d4ff6
> SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*,
> HandlerCallRec*) + 428
> 21  com.apple.HIToolbox   0x7fffd51d4e3f
> SendEventToEventTargetWithOptions + 43
> 22  com.apple.HIToolbox   0x7fffd51f1f9f
> HIView::SendDraw(short, OpaqueGrafPtr*, 

Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Maria Hakonen]

Many thanks for the answer!

Best,
Maria

2017-04-25 21:05 GMT+03:00 Douglas Greve :

> -i{ijk}s will change the voxel size of the columns, rows, and slices,
> respectively
>
> -i{ijk}d will change the direction cosines of the cols, rows, slices
>
>
>
> On 4/25/17 11:47 AM, Maria Hakonen wrote:
>
> Dear Freesurfer experts,
>
> Could someone please let me know what is the meaning of the arguments
> -iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
> From the internet and by typing mri_convert on the command line I only
> managed to find the following information:
>
> -iis, --in_i_size 
> -ijs, --in_j_size 
> -iks, --in_k_size 
> -iid, --in_i_direction   
> -ijd, --in_j_direction   
> -ikd, --in_k_direction   
>
> However, I don't still understand what is the effect of those argumnents
> in the following command:
>
> mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 -iis
> 5 -ijs 5 -iks 5
>
> Are the arguments describing the direction and voxelsize of .bfloat?
>
> Best,
> Maria
>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] mri_cvs_register failure from missing shared lib

[Corinna Bauer]

The comman was mri_cvs_register --mov MAE_06072013 --mni (because labels in
MNI space were mapping incorrectly to subject space -- see this thread
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52786.html )

The log is attached. I killed the command once I saw the errors.

Thanks!

Corinna


On Tue, Apr 25, 2017 at 2:46 PM, Z K  wrote:

> Hi Corinna,
>
> Its been awhile since Ive used Ubuntu12.04. Infact its End of Life date
> is 3 days away ;)
>
> Can you please send me the command and the log file which gives the
> exact error. Thanks.
>
> -Zeke
>
> On 04/25/2017 01:49 PM, Corinna Bauer wrote:
> > Hi Zeke,
> >
> > I am also having this same problem. Even after completing the steps you
> > listed above. I am running Ubuntu 12.04.
> >
> > Any suggetions?
> >
> > Thanks
> >
> > On Wed, May 28, 2014 at 1:50 PM, Z K  > > wrote:
> >
> > You will need to install libboost v1.41 onto your system. You should
> be
> > able to install it using yum:
> >
> > $>yum install boost-devel
> >
> > However, its possible that the version you get thru this method may
> be
> > incompatible with the version required by freesurfer. If the above
> does
> > not fix your issue, then download libboost
> > (http://www.boost.org/users/history/version_1_41_0.html
> > ) and untar
> > it. Then:
> >
> >  >cd libboost_folder
> >  >mkdir libraries
> >  >./bootstrap.sh --prefix=./libraries
> >  >./bjam install
> >  >cd libraries/lib
> >  > ln -s libboost_program_options.so.1.41.0
> > libboost_program_options.so.5
> >  >export
> > LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/
> lib:$LD_LIBRARY_PATH
> >
> > Hope this helps and feel free to contact me if your having issues
> > getting it to work.
> >
> > -Zeke
> >
> > On 05/28/2014 12:17 PM, Michael Waskom wrote:
> > > Hi, I had mri_cvs_register die on me when it couldn't find a shared
> > > library. Relevant bit is (full log is attached):
> > >
> > > mris_resample: error while loading shared libraries:
> > > libboost_program_options.so.5: cannot open shared object file: No
> such
> > > file or directory
> > >
> > > Freesurfer bugr info:
> > >
> > > 
> > >
> > > FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0
> > >
> > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > >
> > > RedHat release: Red Hat Enterprise Linux Server release 6.3
> (Santiago)
> > >
> > > Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64
> > >
> > > --
> > >
> > > Any thoughts on how to proceed? Thanks!
> > >
> > > Michael
> > >
> > >
> > > ___
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> > > Freesurfer@nmr.mgh.harvard.edu  harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu  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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Logfile for mri_cvs_register
Tue Apr 25 15:30:27 EDT 2017
--mov MAE_06072013 --mni
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
bauer
Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
asegfname aseg
Using m3z type morph files.
mris_resample --atlas_reg /usr/local/freesurfer/subjects//cvs_avg35_inMNI152/surf/lh.sphere --annot_in /drobo2/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/label/lh.aparc.annot --annot_out 

Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

[Douglas Greve]

The missing/extra are due to sub-1mm estimation. They do not exist 
independently. If you want to avoid partially volumed voxels, you can 
erode the segmentation to remove border voxels



On 4/25/17 2:50 PM, Gamaliz wrote:

For example.
I register another image to the aseg+aparc file and do some 
pixel-by-pixel calculations; reading the regions from the aseg+aparc 
and matching them on the registered file (in this case a DTI) ie: 
every pixel with value 2 in aseg+aparc belongs to the 
Left-Cerebral-White-Matter region.


however, as the aseg+aparc is missing some pixels (or have extra ones) 
depending on how the pixel count differs from the volume (as reported 
in the aseg.stats file), I will have either missing (extra) pixels.



Maybe I am asking too much? :/


On Tue, Apr 25, 2017 at 2:45 PM, Douglas Greve 
> wrote:


more exact than what?


On 4/25/17 2:07 PM, Gamaliz wrote:

Is there any way to generate a file which is more exact? Or
perhaps, is that file already there?

On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve
> wrote:

The aseg.stats is generated with partial volume estimation


On 4/25/17 12:40 PM, Gamaliz wrote:

I wrote an algorithm which uses the number of pixels per
region in the aseg+aparc.mgz file. As this file has 1x1x1mm3
I was expecting the number of pixels to match very closely
the value of the volume; as each pixel represents a 1 mm3
cube.(I did the same for cortical volume and got a similar
result, with an even larger discrepancy).

The aseg.stats file lists the nVoxel value, and it is
basically the volume rounded up.
here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz):
7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in
aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz):5899

Pretty much the values are close to the volume, but
different enough to be significant. I wonder why this
discrepancy.


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 The
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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

[Gamaliz]

For example.
I register another image to the aseg+aparc file and do some pixel-by-pixel
calculations; reading the regions from the aseg+aparc and matching them on
the registered file (in this case a DTI) ie: every pixel with value 2 in
aseg+aparc belongs to the Left-Cerebral-White-Matter region.

however, as the aseg+aparc is missing some pixels (or have extra ones)
depending on how the pixel count differs from the volume (as reported in
the aseg.stats file), I will have either missing (extra) pixels.


Maybe I am asking too much? :/


On Tue, Apr 25, 2017 at 2:45 PM, Douglas Greve 
wrote:

> more exact than what?
>
> On 4/25/17 2:07 PM, Gamaliz wrote:
>
> Is there any way to generate a file which is more exact? Or perhaps, is
> that file already there?
>
> On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve 
> wrote:
>
>> The aseg.stats is generated with partial volume estimation
>>
>> On 4/25/17 12:40 PM, Gamaliz wrote:
>>
>> I wrote an algorithm which uses the number of pixels per region in the
>> aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
>> of pixels to match very closely the value of the volume; as each pixel
>> represents a 1 mm3 cube.(I did the same for cortical volume and got a
>> similar result, with an even larger discrepancy).
>>
>> The aseg.stats file lists the nVoxel value, and it is basically the
>> volume rounded up.
>> here are some sample values for subcortical regions:
>>
>> Left-Lateral-Ventricle Volume (mm3): 7829.8
>> Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
>> Left-Inf-Lat-Vent Volume (mm3):594
>> Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
>> Left-Cerebellum-White-Matter Volume (mm3):12668
>> Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
>> Left-Cerebellum-Cortex Volume (mm3):44113.2
>> Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804
>> Left-Thalamus-Proper Volume (mm3):5752.8
>> Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899
>>
>> Pretty much the values are close to the volume, but different enough to
>> be significant. I wonder why this discrepancy.
>>
>>
>> ___
>> Freesurfer mailing 
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>>
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>> du/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.
>
> --
> gAbE
>
> ___
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] mri_cvs_register failure from missing shared lib

[Z K]

Hi Corinna,

Its been awhile since Ive used Ubuntu12.04. Infact its End of Life date 
is 3 days away ;)

Can you please send me the command and the log file which gives the 
exact error. Thanks.

-Zeke

On 04/25/2017 01:49 PM, Corinna Bauer wrote:
> Hi Zeke,
>
> I am also having this same problem. Even after completing the steps you
> listed above. I am running Ubuntu 12.04.
>
> Any suggetions?
>
> Thanks
>
> On Wed, May 28, 2014 at 1:50 PM, Z K  > wrote:
>
> You will need to install libboost v1.41 onto your system. You should be
> able to install it using yum:
>
> $>yum install boost-devel
>
> However, its possible that the version you get thru this method may be
> incompatible with the version required by freesurfer. If the above does
> not fix your issue, then download libboost
> (http://www.boost.org/users/history/version_1_41_0.html
> ) and untar
> it. Then:
>
>  >cd libboost_folder
>  >mkdir libraries
>  >./bootstrap.sh --prefix=./libraries
>  >./bjam install
>  >cd libraries/lib
>  > ln -s libboost_program_options.so.1.41.0
> libboost_program_options.so.5
>  >export
> LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH
>
> Hope this helps and feel free to contact me if your having issues
> getting it to work.
>
> -Zeke
>
> On 05/28/2014 12:17 PM, Michael Waskom wrote:
> > Hi, I had mri_cvs_register die on me when it couldn't find a shared
> > library. Relevant bit is (full log is attached):
> >
> > mris_resample: error while loading shared libraries:
> > libboost_program_options.so.5: cannot open shared object file: No such
> > file or directory
> >
> > Freesurfer bugr info:
> >
> > 
> >
> > FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0
> >
> > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> >
> > RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago)
> >
> > Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64
> >
> > --
> >
> > Any thoughts on how to proceed? Thanks!
> >
> > Michael
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> >
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> 
>
>
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> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

[Douglas Greve]

more exact than what?


On 4/25/17 2:07 PM, Gamaliz wrote:
Is there any way to generate a file which is more exact? Or perhaps, 
is that file already there?


On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve 
> wrote:


The aseg.stats is generated with partial volume estimation


On 4/25/17 12:40 PM, Gamaliz wrote:

I wrote an algorithm which uses the number of pixels per region
in the aseg+aparc.mgz file. As this file has 1x1x1mm3 I was
expecting the number of pixels to match very closely the value of
the volume; as each pixel represents a 1 mm3 cube.(I did the same
for cortical volume and got a similar result, with an even larger
discrepancy).

The aseg.stats file lists the nVoxel value, and it is basically
the volume rounded up.
here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in
aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz):5899

Pretty much the values are close to the volume, but different
enough to be significant. I wonder why this discrepancy.


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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

[Gamaliz]

Is there any way to generate a file which is more exact? Or perhaps, is
that file already there?

On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve 
wrote:

> The aseg.stats is generated with partial volume estimation
>
> On 4/25/17 12:40 PM, Gamaliz wrote:
>
> I wrote an algorithm which uses the number of pixels per region in the
> aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
> of pixels to match very closely the value of the volume; as each pixel
> represents a 1 mm3 cube.(I did the same for cortical volume and got a
> similar result, with an even larger discrepancy).
>
> The aseg.stats file lists the nVoxel value, and it is basically the volume
> rounded up.
> here are some sample values for subcortical regions:
>
> Left-Lateral-Ventricle Volume (mm3): 7829.8
> Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
> Left-Inf-Lat-Vent Volume (mm3):594
> Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
> Left-Cerebellum-White-Matter Volume (mm3):12668
> Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
> Left-Cerebellum-Cortex Volume (mm3):44113.2
> Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804
> Left-Thalamus-Proper Volume (mm3):5752.8
> Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899
>
> Pretty much the values are close to the volume, but different enough to be
> significant. I wonder why this discrepancy.
>
>
> ___
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Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Douglas Greve]

-i{ijk}s will change the voxel size of the columns, rows, and slices, 
respectively


-i{ijk}d will change the direction cosines of the cols, rows, slices



On 4/25/17 11:47 AM, Maria Hakonen wrote:

Dear Freesurfer experts,

Could someone please let me know what is the meaning of the arguments 
-iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
From the internet and by typing mri_convert on the command line I only 
managed to find the following information:


-iis, --in_i_size 
-ijs, --in_j_size 
-iks, --in_k_size 
-iid, --in_i_direction   
-ijd, --in_j_direction   
-ikd, --in_k_direction   

However, I don't still understand what is the effect of those 
argumnents in the following command:


mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 
-iis 5 -ijs 5 -iks 5


Are the arguments describing the direction and voxelsize of .bfloat?

Best,
Maria


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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

[Douglas Greve]

The aseg.stats is generated with partial volume estimation


On 4/25/17 12:40 PM, Gamaliz wrote:
I wrote an algorithm which uses the number of pixels per region in the 
aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the 
number of pixels to match very closely the value of the volume; as 
each pixel represents a 1 mm3 cube.(I did the same for cortical volume 
and got a similar result, with an even larger discrepancy).


The aseg.stats file lists the nVoxel value, and it is basically the 
volume rounded up.

here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz):5899

Pretty much the values are close to the volume, but different enough 
to be significant. I wonder why this discrepancy.



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Re: [Freesurfer] mri_cvs_register failure from missing shared lib

[Corinna Bauer]

Hi Zeke,

I am also having this same problem. Even after completing the steps you
listed above. I am running Ubuntu 12.04.

Any suggetions?

Thanks

On Wed, May 28, 2014 at 1:50 PM, Z K  wrote:

> You will need to install libboost v1.41 onto your system. You should be
> able to install it using yum:
>
> $>yum install boost-devel
>
> However, its possible that the version you get thru this method may be
> incompatible with the version required by freesurfer. If the above does
> not fix your issue, then download libboost
> (http://www.boost.org/users/history/version_1_41_0.html) and untar it.
> Then:
>
>  >cd libboost_folder
>  >mkdir libraries
>  >./bootstrap.sh --prefix=./libraries
>  >./bjam install
>  >cd libraries/lib
>  > ln -s libboost_program_options.so.1.41.0 libboost_program_options.so.5
>  >export
> LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH
>
> Hope this helps and feel free to contact me if your having issues
> getting it to work.
>
> -Zeke
>
> On 05/28/2014 12:17 PM, Michael Waskom wrote:
> > Hi, I had mri_cvs_register die on me when it couldn't find a shared
> > library. Relevant bit is (full log is attached):
> >
> > mris_resample: error while loading shared libraries:
> > libboost_program_options.so.5: cannot open shared object file: No such
> > file or directory
> >
> > Freesurfer bugr info:
> >
> > 
> >
> > FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0
> >
> > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> >
> > RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago)
> >
> > Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64
> >
> > --
> >
> > Any thoughts on how to proceed? Thanks!
> >
> > Michael
> >
> >
> > ___
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[Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

[Gamaliz]

I wrote an algorithm which uses the number of pixels per region in the
aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
of pixels to match very closely the value of the volume; as each pixel
represents a 1 mm3 cube.(I did the same for cortical volume and got a
similar result, with an even larger discrepancy).

The aseg.stats file lists the nVoxel value, and it is basically the volume
rounded up.
here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899

Pretty much the values are close to the volume, but different enough to be
significant. I wonder why this discrepancy.
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[Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

[Maria Hakonen]

Dear Freesurfer experts,

Could someone please let me know what is the meaning of the arguments -iid,
-ijd, -ikd, -iis, -ijs, and -iks of mri_covert?
>From the internet and by typing mri_convert on the command line I only
managed to find the following information:

-iis, --in_i_size 
-ijs, --in_j_size 
-iks, --in_k_size 
-iid, --in_i_direction   
-ijd, --in_j_direction   
-ikd, --in_k_direction   

However, I don't still understand what is the effect of those argumnents in
the following command:

mri_convert gre_000.bfloat data.mgh -iid 1 0 0 -ijd 0 -1 0 -ikd 0 0 1 -iis
5 -ijs 5 -iks 5

Are the arguments describing the direction and voxelsize of .bfloat?

Best,
Maria
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Re: [Freesurfer] Additional processing flags when using the longitudinal pipeline

[Martin Reuter]

Hi Gustav,


use -all and -mprage for all steps

use -qcache and -hippo..subfields only in the -long step.


Best, Martin



On 04/25/2017 12:51 PM, Gustav Mårtensson wrote:

Hi,

I have a question regarding the longitudinal pipeline.

We are following the workflow summary as outlined in 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, 
essentially:


1. recon-all -all -s  -i path_to_tpN_dcm

2. recon-all -base  -tp  -tp  ... -all

3. recon-all -long   -all

We tend to run -all -mprage -qcache -hippocampal-subfields-T1 
-brainstem-structures in our cross-sectional process. Should we use 
all (or part of) these options for step 2 and 3?


We are running on Ubuntu 16.04 LTS with FS version 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.


Thank you for your help!

Gustav Mårtensson
--
*Gustav Mårtensson* | PhD student
Division of Clinical Geriatrics
Department of Neurobiology, Care Sciences and Society
Karolinska Institutet
___
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[Freesurfer] Additional processing flags when using the longitudinal pipeline

[Gustav Mårtensson]

Hi,

I have a question regarding the longitudinal pipeline.

We are following the workflow summary as outlined in 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, essentially:

1. recon-all -all -s  -i path_to_tpN_dcm

2. recon-all -base  -tp  -tp  ... -all

3. recon-all -long   -all

We tend to run -all -mprage -qcache -hippocampal-subfields-T1 
-brainstem-structures in our cross-sectional process. Should we use all (or 
part of) these options for step 2 and 3?

We are running on Ubuntu 16.04 LTS with FS version 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

Thank you for your help!

Gustav Mårtensson
--
Gustav Mårtensson | PhD student
Division of Clinical Geriatrics
Department of Neurobiology, Care Sciences and Society
Karolinska Institutet
___
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Re: [Freesurfer] REPOST: Two stage model question

[Clara Kühn]

Hi Martin,

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

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

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


Thanks for your help!
Clara



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

Hi Clara, 

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

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

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

Best, Martin

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


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Re: [Freesurfer] TRACULA tract reconstruction

[Joëlle Ismay Rosanne Van Der Molen]

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


Best,

Joëlle


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

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

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

Best,
a.y


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


Hi Anastasia,


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


Best,


Joëlle




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

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

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

Best,
a.y

From: 
>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
>
Reply-To: Freesurfer support list 
>
Date: Friday, March 31, 2017 at 7:44 AM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] TRACULA tract reconstruction


​Hi Anastasia,


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


Best,


Joëlle


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

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

a.y


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


​Hi Barbara,


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

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


Best,

Joëlle


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 de la part de Barbara Kreilkamp 
>
Envoyé : mercredi 29 mars 2017 14:18
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction


Hi Joëlle,

Which scanner was used to acquire the images? I have used Osirix light in the 
past to anonymize my dicom images, maybe you'd like to try that?

Best wishes,

Barbara

On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote:

​Hi Anastasia,


Yes, I use dicom images as input for Tracula. I also specify the bvecs files, 
as Tracula returns an error if I try to run it with a configuration file that 
does not contain them.



Unfortunately, our dicom images are not anonymised, so I cannot provide them.


Best,


Joëlle



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

 de la part de Yendiki, Anastasia 

Envoyé : mercredi 22 mars 2017 15:40
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle – What images do you pass as input to TRACULA? Do you pass the dicom 

Re: [Freesurfer] TRACULA tract reconstruction

[Yendiki, Anastasia]

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

Best,
a.y


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


Hi Anastasia,


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


Best,


Joëlle




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

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

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

Best,
a.y

From: 
>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
>
Reply-To: Freesurfer support list 
>
Date: Friday, March 31, 2017 at 7:44 AM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] TRACULA tract reconstruction


​Hi Anastasia,


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


Best,


Joëlle


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

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

a.y


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


​Hi Barbara,


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

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


Best,

Joëlle


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 de la part de Barbara Kreilkamp 
>
Envoyé : mercredi 29 mars 2017 14:18
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction


Hi Joëlle,

Which scanner was used to acquire the images? I have used Osirix light in the 
past to anonymize my dicom images, maybe you'd like to try that?

Best wishes,

Barbara

On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote:

​Hi Anastasia,


Yes, I use dicom images as input for Tracula. I also specify the bvecs files, 
as Tracula returns an error if I try to run it with a configuration file that 
does not contain them.



Unfortunately, our dicom images are not anonymised, so I cannot provide them.


Best,


Joëlle



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

 de la part de Yendiki, Anastasia 

Envoyé : mercredi 22 mars 2017 15:40
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle – What images do you pass as input to TRACULA? Do you pass the dicom 
itself, or a converted file? Happy to look at your dicom, if it’s anonymized.

a.y

From: 
>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
>
Reply-To: Freesurfer support list 

Re: [Freesurfer] TRACULA tract reconstruction

[Joëlle Ismay Rosanne Van Der Molen]

Hi Anastasia,


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


Best,


Joëlle




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

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

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

Best,
a.y

From: 
>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
>
Reply-To: Freesurfer support list 
>
Date: Friday, March 31, 2017 at 7:44 AM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] TRACULA tract reconstruction


​Hi Anastasia,


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


Best,


Joëlle


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

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

a.y


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


​Hi Barbara,


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

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


Best,

Joëlle


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 de la part de Barbara Kreilkamp 
>
Envoyé : mercredi 29 mars 2017 14:18
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction


Hi Joëlle,

Which scanner was used to acquire the images? I have used Osirix light in the 
past to anonymize my dicom images, maybe you'd like to try that?

Best wishes,

Barbara

On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote:

​Hi Anastasia,


Yes, I use dicom images as input for Tracula. I also specify the bvecs files, 
as Tracula returns an error if I try to run it with a configuration file that 
does not contain them.



Unfortunately, our dicom images are not anonymised, so I cannot provide them.


Best,


Joëlle



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

 de la part de Yendiki, Anastasia 

Envoyé : mercredi 22 mars 2017 15:40
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle – What images do you pass as input to TRACULA? Do you pass the dicom 
itself, or a converted file? Happy to look at your dicom, if it’s anonymized.

a.y

From: 
>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, March 22, 2017 at 3:55 AM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] TRACULA tract reconstruction

Hi Anastasia and Antonin,

I apologize for the late response.
Thank you very much for the explanations!

Regarding the gradient tables, I realized that I was indeed using the old 
version of mrtrix3, and was getting tables with a flipped x component (sign 
inversion), 

[Freesurfer] fs6.0 mri_surf2surf failure

[Dongnandi]

Dear FS experts,

 I'm trying to transform some files from fsaverage space to
fsaverage5 space using mri_surf2surf(fs version: 6.0), however, it is weird
that the results turn out to be all zeros on the fsaverage5 surface, the
command line I used if : mri_surf2surf -srcsubject fsaverage -sval
${hemi}.fsaverage.nii.gz -hemi ${hemi}  --cortex -trgsubject fsaverage5
-tval ${hemi}.fsaverage5.nii.gz -surfreg sphere.reg. There is no error
reported.

 The strange thing is that it works well using FS5.3, it failed
after I update to FS 6.0. Any suggestion of solving this?

 Many thanks!

 Best!

 Dong

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.