Re: [Freesurfer] T2pial shrinks pial surface

[Chris Adamson]

Thanks Bruce,

Doing the bias correct and -odt float fixed the issue. Adding -odt short did 
not.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, 8 March 2016 11:46 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

it might, but you will need to make some fixes that are in 6.0 (soon) but not 
in 5.3. The 5.3 recon-all changes the T2 datatype to uchar when it resamples it 
to be in register with the T1. You should change that line to have -odt short 
or -odt float so that it doesn't saturate at 255, which is what caused the 
original problem.

On Tue, 8 Mar 2016, Chris Adamson wrote:

> I see it now. I will try to perform a bias correction on the image prior to 
> importing and see if that helps. Thanks Bruce.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Tuesday, 8 March 2016 4:23 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>
> Hi Chris
>
> I took a look,  and the problem is that there are big changes in contrast 
> between occipital and frontal lobes. If we normalize both posterior and 
> frontal wm to 110, occipital gray matter gets mapped to 180 but frontal gray 
> gets >255. This kind of thing can be caused by a transmit "bias"
> field, or by dielectric effects.  I'm not sure why this is a problem 
> with this dataset and not others
>
> cheers
> Bruce
>
> On Mon, 7 Mar 2016, Chris Adamson wrote:
>
>> Thanks Bruce.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris 
>> Adamson
>> Sent: Monday, 7 March 2016 1:54 PM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>>
>> It is checkT2pial.zip
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>> Fischl
>> Sent: Monday, 7 March 2016 1:35 PM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>> On Mon, 7 Mar
>> 2016, Chris Adamson wrote:
>>
>>> How can I upload it to you?
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>>> Fischl
>>> Sent: Monday, 7 March 2016 1:25 PM
>>> To: Freesurfer support list 
>>> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>>>
>>> Hi Chris
>>>
>>> if you upload that dataset I'll try to take a look soon
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 7 Mar 2016, Chris Adamson wrote:
>>>

 The T2pial option mostly works beautifully. I have a few cases 
 where the pial surface just shrinks globally and wraps over the 
 white surface (see attached). I have checked the T2.mgz and the 
 registration with the T1 is fine. This happens sometimes in one hemisphere 
 only.

 Any ideas?

  

 [IMAGE]

 Chris Adamson
 Senior Research Officer
 Developmental Imaging
 Murdoch Childrens Research Institute The Royal Children’s Hospital 
 Flemington Rd Parkville, Victoria 3052 AUS
 T: (03) 9936 6780
 E: chris.adam...@mcri.edu.au
 www.mcri.edu.au

  

 [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]

  

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 return e-mail, and do not read, copy, retransmit or otherwise deal 
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 Murdoch Childrens Research Institute
 (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does 
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[Freesurfer] Position at UW (fwd)

[Bruce Fischl]

FYI

-- Forwarded message --
Date: Tue, 8 Mar 2016 02:00:35 +
From: THOMAS J. GRABOWSKI 
To: Bruce Fischl 
Subject: Position at UW


Hi Bruce,


I am looking for a research scientist with expertise in fMRI experimental
design and neuroscience to fill an unexpected vacancy at our Integrated
Brain Imaging Center at the University of Washington
(http://www.ibic.washington.edu). 

 

This is a key position in our group, and I am reaching out to peer labs to
find someone with the necessary expertise and professionalism.  It’s a nice
opportunity to join a friendly, diverse and smart group in an outstanding
university setting.

 

The successful applicant would essentially function as our technical lab
manager, and serve as a research navigator for collaborators who want an
imaging partner.   

 

If anyone who comes to mind as being a good match, here is the link to our
ad:

 

https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szCategory=
jobprofile&szOrderID=128007

 

I would appreciate any interest!

 

All the best,


Tom


---

Thomas J. Grabowski, Jr, MD
Professor of Radiology and Joint Professor of Neurology
Director, UW Integrated Brain Imaging Center
Director, UW Medicine Memory and Brain Wellness Center
University of Washington School of Medicine
Seattle WA  98195
(206) 616-0021 (voice)
(206) 685-0457 (asst)
tgra...@uw.edu 


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Re: [Freesurfer] Medial crossing surfaces

[maryam koochaki]

Hi Bruce,Thanks, I uploaded my subject in your ftp site.case name: 
train_emc_010.tar.gz
Best,Maryam
 






 

   

 On Monday, March 7, 2016 5:26 AM, Bruce Fischl  
wrote:
 

 Hi Maryam

I guess, although it's hard to say without looking at your data. I think 
the upcoming V6 does much better on the midline. If you upload your 
data I can take a look. For the command line you can check out the 
recon-all help and just rerun the pial surface generation

cheers
Bruce
On Mon, 7 Mar 2016, maryam koochaki wrote:

>  Hi Bruce,
> I am editing aseg to correct the boundaries that excluded the lateral
> ventricle. The problem with lateral ventricle has been solved after running
> the process with -noaseg flag.
> But the boundaries in the middle, is crossing to the other hemesphere in
> some cases.
> 
> I even tried -autorecon2-cp, the problem still exists.
> aparc+aseg has not been updated after running the process.
> 
> Does Celine's case apply to mine? Here is your answer to Celine:
> 
> Hi Celine
> the only existing way to correct this would be to create two volumes in
> addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and
> rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the
> contralateral hemisphere that are causing problems, then rerun
> mris_make_surfaces for each hemi, using the appropriate volume. At some
> point I guess we should put an intersection check into it for the contra
> hemi
> cheers
> Bruce
> 
> Could you help me with the exact command line? 
> 
> Thank you in advance for your help,
> Maryam
> 
> 
>  
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[R Edgar]

On 7 March 2016 at 11:25, Francis Tyson Thomas
 wrote:

> That information was a lot helpful. At this point I'm currently trying to
> reduce the recon-all processing time as much as possible and for this reason
> I was looking to get the -use-gpu flag working. I'm currently running a
> freesurfer v6 beta version on Ubuntu 14.04.4. With regard to the graphic
> card it is a dual K2200 configuration (I guess they are running in sli
> configuration - although I'm not completely sure).
>
> When you mentioned you compiled everything, I believe you were referring to
> compiling CUDA 7.5 for Ubuntu 14.04. Because after seeing the link -
> https://developer.nvidia.com/cuda-gpus
> -  we settled for CUDA 5 since it was the compatible version mentioned for
> K2200. Does that mean CUDA 7.5 is backwards compatible with a slight
> tinkering and can be used with freesurfer 6.0 ?

I think that you might have misunderstood the NVIDIA page.

It lists the K2200 as a Compute Capability 5 GPU (just like my K1200).
The Compute Capability refers to the hardware:
http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#compute-capabilities
Compute capability 5 is also called "Maxwell," while the work I did on
Freesurfer was around the time of Compute Capability 2, known as
Fermi. In CPU terms, GPU compute capabilities are a bit like Ivy
Bridge vs Sandy Bridge (although I think that GPU features vary more
than the CPU ones).

In order to program the GPU, you need the NVIDIA CUDA Toolkit, which
contains the required compiler (nvcc). The current version of this is
7.5. I installed it by following the instructions on NVIDIA's website:
http://docs.nvidia.com/cuda/index.html
This was quite straightforward (certainly moreso than it was five or
six years ago, when you could never be sure that your X11.conf would
survive).

Either with the toolkit, or as a separate install, you can get a lot
of examples from NVIDIA. I'd suggest grabbing those, and making sure
that you can compile them. The "DeviceQuery" one will probe your PCIe
bus, and report what GPUs it finds.

> I however tried to setup CUDA 5 following the instructions in the link -
> http://www.unixmen.com/how-to-install-cuda-5-0-toolkit-in-ubuntu/ - however,
> I'm not able to get it running. I keep getting the following error "Unable
> to acquire CUDA device". Does this sound familiar ?

I suspect (although I wasn't following things at the time) that the
Toolkit v5 was before Maxwell cards were released. If so, then it
wouldn't know what to do with the GPUs.

For the record, since I was writing the CUDA bits so long ago (for the
volume side of things - I didn't do the surface accelerations), they
only use Fermi features. For this reason, you'll want to make sure
that you have --enable-fermi-gpu when you run configure (and make sure
that it's picking out your CUDA installation - I had to tweak the
configure script for this).

> If you can share some more information in setting this up it will be great
> since the amount of time recon-all takes is quite too long for running
> multiple datasets. Most importantly we are concerned about the hippocampal
> segmentation in freesurfer 6 rather than recon-all and so speeding this up
> would be extremely helpful.

I don't know if those portions benefit from CUDA acceleration at this
time. I focused on mri_em_register and mri_ca_register. Even if other
programs (which ones are they?) can be linked against some of the
accelerated routines, there is no guarantee of speed up - the time to
shuffle data to and from the GPU is typically greater than the speedup
of any one routine.

Hope this helps,

Richard
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Re: [Freesurfer] T2pial shrinks pial surface

[Bruce Fischl]

it might, but you will need to make some fixes that are in 6.0 (soon) but 
not in 5.3. The 5.3 recon-all changes the T2 datatype to uchar when it 
resamples it to be in register with the T1. You should change that line to 
have -odt short or -odt float so that it doesn't saturate at 255, which is 
what caused the original problem.


On Tue, 8 Mar 2016, Chris Adamson wrote:


I see it now. I will try to perform a bias correction on the image prior to 
importing and see if that helps. Thanks Bruce.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, 8 March 2016 4:23 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

Hi Chris

I took a look,  and the problem is that there are big changes in contrast between occipital 
and frontal lobes. If we normalize both posterior and frontal wm to 110, occipital gray 
matter gets mapped to 180 but frontal gray gets >255. This kind of thing can be caused by 
a transmit "bias"
field, or by dielectric effects.  I'm not sure why this is a problem with this 
dataset and not others

cheers
Bruce

On Mon, 7 Mar 2016, Chris Adamson wrote:


Thanks Bruce.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris
Adamson
Sent: Monday, 7 March 2016 1:54 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

It is checkT2pial.zip

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Monday, 7 March 2016 1:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Mon, 7 Mar
2016, Chris Adamson wrote:


How can I upload it to you?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Monday, 7 March 2016 1:25 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

Hi Chris

if you upload that dataset I'll try to take a look soon

cheers
Bruce


On Mon, 7 Mar 2016, Chris Adamson wrote:



The T2pial option mostly works beautifully. I have a few cases where
the pial surface just shrinks globally and wraps over the white
surface (see attached). I have checked the T2.mgz and the
registration with the T1 is fine. This happens sometimes in one hemisphere only.

Any ideas?

 

[IMAGE]

Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute The Royal Children’s Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au

 

[IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]

 

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Murdoch Childrens Research Institute
(MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does
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in the Communication, computer virus, data corruption, interference
or delay arising from or in respect of the Communication.

 

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Re: [Freesurfer] T2pial shrinks pial surface

[Chris Adamson]

I see it now. I will try to perform a bias correction on the image prior to 
importing and see if that helps. Thanks Bruce.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, 8 March 2016 4:23 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

Hi Chris

I took a look,  and the problem is that there are big changes in contrast 
between occipital and frontal lobes. If we normalize both posterior and frontal 
wm to 110, occipital gray matter gets mapped to 180 but frontal gray gets >255. 
This kind of thing can be caused by a transmit "bias" 
field, or by dielectric effects.  I'm not sure why this is a problem with this 
dataset and not others

cheers
Bruce

On Mon, 7 Mar 2016, Chris Adamson wrote:

> Thanks Bruce.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris 
> Adamson
> Sent: Monday, 7 March 2016 1:54 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>
> It is checkT2pial.zip
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Monday, 7 March 2016 1:35 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
> On Mon, 7 Mar
> 2016, Chris Adamson wrote:
>
>> How can I upload it to you?
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>> Fischl
>> Sent: Monday, 7 March 2016 1:25 PM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>>
>> Hi Chris
>>
>> if you upload that dataset I'll try to take a look soon
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 7 Mar 2016, Chris Adamson wrote:
>>
>>>
>>> The T2pial option mostly works beautifully. I have a few cases where 
>>> the pial surface just shrinks globally and wraps over the white 
>>> surface (see attached). I have checked the T2.mgz and the 
>>> registration with the T1 is fine. This happens sometimes in one hemisphere 
>>> only.
>>>
>>> Any ideas?
>>>
>>>  
>>>
>>> [IMAGE]
>>>
>>> Chris Adamson
>>> Senior Research Officer
>>> Developmental Imaging
>>> Murdoch Childrens Research Institute The Royal Children’s Hospital 
>>> Flemington Rd Parkville, Victoria 3052 AUS
>>> T: (03) 9936 6780
>>> E: chris.adam...@mcri.edu.au
>>> www.mcri.edu.au
>>>
>>>  
>>>
>>> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]
>>>
>>>  
>>>
>>> This e-mail and any attachments to it (the "Communication") are, 
>>> unless otherwise stated, confidential, may contain copyright 
>>> material and is for the use only of the intended recipient. If you 
>>> receive the Communication in error, please notify the sender 
>>> immediately by return e-mail, delete the Communication and the 
>>> return e-mail, and do not read, copy, retransmit or otherwise deal 
>>> with it. Any views expressed in the Communication are those of the 
>>> individual sender only, unless expressly stated to be those of 
>>> Murdoch Childrens Research Institute
>>> (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does 
>>> not accept liability in connection with the integrity of or errors 
>>> in the Communication, computer virus, data corruption, interference 
>>> or delay arising from or in respect of the Communication.
>>>
>>>  
>>>
>>> P Please consider the environment before printing this email
>>>
>>>  
>>>
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Re: [Freesurfer] How to find the difference between to different fMRI datasets?

[Douglas N Greve]

On 03/04/2016 06:01 AM, Silas wrote:
> Thanks Douglas!
>
> 1 - I have two functional files per subject (.mgh). Is it possible to insert 
> two files per subject in mris_preproc? In my former functional analysis I 
> haven't concatenated my data using a FSGD-file when running mris_preproc.
Are these volumes or surfaces? If volumes, get a registration matrix 
using bbregister, then run mri_vol2surf specifying fsaverage as the 
target subject. If a surface, then use mri_surf2surf.
>
> 2 - Can you calculate the difference between two functional data sets (on the 
> fsaverage) before starting the group analysis stream? E.g. by subtracting the 
> files?
Yes, fscalc file1.mgh sub file2.mgh -o diff.mgh
>
> Best, Silas
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Thursday, March 3, 2016 6:19 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] How to find the difference between to different 
> fMRI datasets?
>
> Create a contrast between the two conditions
>
> On 03/01/2016 01:27 AM, Silas wrote:
>> Dear FreeSurfer team,
>>
>>
>> Thank you for all your help so far!
>>
>>
>> I would like to visualize the difference between two fMRI data sets.
>>
>> Data set1: Cortical activation during movement of a finger.
>>
>> Data set2: Cortical activation during movement of a finger different
>> from the first finger.
>>
>>
>> How can i perform this operation?
>>
>>
>> Best, Silas
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> 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 
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> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
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>
>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Cortical thickness using freesurfer

[Douglas N Greve]

is this still a problem?

On 03/04/2016 01:24 PM, Sahil Bajaj wrote:
> Dear all,
>
> I am working on calculation of cortical thickness from a set of 
> subjects. I am following the instructions from 
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and 
> I am able to run up-to step-2 successfully i.e. I can display the ROIs 
> on fsaverage subject volume. But when I run step-3 using:
>
> *mri_vol2surf --mov /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii 
> --reg TT.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out 
> ROI5.mgh --reshape*
>
>
> It runs as follow:
>
> (here lh_cuneus.nii is one of the ROIs,FTD_Data is my subject 
> directory for FreeSurfer and S01_LP is the output folder for one of 
> the subjects after running recon -all)
>
>
> srcvol = /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii
> srcreg = TT.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> ProjDist = 0.5
> reshape = 1
> interp = nearest
> float2int = round
> GetProjMax = 1
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Reading surface /media/Storage/FTD_Data/fsaverage/surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 1
> using old
>  2 0.1 0 1
> using old
>  3 0.2 0 1
> using old
>  4 0.3 0 1
> using old
>  5 0.4 0 1
> using old
>  6 0.5 0 1
> using old
>  7 0.6 0 1
> using old
>  8 0.7 0 1
> using old
>  9 0.8 0 1
> using old
> 10 0.9 0 1
> using old
> Done mapping volume to surface
> Number of source voxels hit = 75054
> Reshaping 7 (nvertices = 163842)
> Writing to ROI5.mgh
> Dim: 23406 1 7
>
>
> Although I don't see any error here but when I display using:
>
> *tksurfer fsaverage lh inflated -overlay ROI5.mgh -fthresh 0.5*
>
> it runs as follow:
>
> setting fthresh to 0.5000
> subject is fsaverage
> hemiis lh
> surface is inflated
> surfer: current subjects dir: /media/Storage/FTD_Data
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /media/Storage/FTD_Data/fsaverage/surf
> checking for nofix files in 'inflated'
> Reading image info (/media/Storage/FTD_Data/fsaverage)
> Reading /media/Storage/FTD_Data/fsaverage/mri/orig.mgz
> surfer: Reading header info from 
> /media/Storage/FTD_Data/fsaverage/mri/orig.mgz
> surfer: vertices=163842, faces=327680
> tkmedit: Trying to open ROI5.dat
> surfer: Interpreting overlay volume ROI5.mgh as encoded scalar volume.
> surfer: curvature read: min=-0.673989 max=0.540227
> surfer: single buffered window
> surfer: tkoInitWindow(fsaverage)
> surfer: using interface 
> /home/sahil/Softwares/freesurfer/tktools/tksurfer.tcl
> Reading /home/sahil/Softwares/freesurfer/tktools/tkm_common.tcl
> Reading /home/sahil/Softwares/freesurfer/tktools/tkm_wrappers.tcl
> Reading /home/sahil/Softwares/freesurfer/lib/tcl/fsgdfPlot.tcl
> Reading /home/sahil/Softwares/freesurfer/tktools/tkUtils.tcl
> Successfully parsed tksurfer.tcl
> reading white matter vertex locations...
>
>
> Again, I don't see any error here. But ROI ROI5.mgh is not displayed 
> on the fsaverage surface. I tried to overlay ROI5.mgh on lh inflated 
> using freeview as well but ROI5.mgh is nowhere.
>
>
> I would really appreciate any help.
>
>
> Thanks,
>
> Sahil
> -- 
> -
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> Office: 713-363-9003
> E-mail:sahil.ne...@gmail.com 
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] error - mri_nu_correct.mni

[Douglas N Greve]

what happens when you run the following?

cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
--i orig.mgz --o orig_nu.mgz



On 03/07/2016 04:09 PM, Flavia Niccolini new wrote:
> Hello,
>
> I was wondering whether you could help with this error:
>
> #
> #@# MotionCor Thu Mar  3 11:35:51 GMT 2016
> Found 1 runs
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
>
>  cp 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1
>
>  mri_convert 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
> --conform
>
> mri_convert 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
> --conform
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (-0, -0, 1)
> Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
> Data is conformed to 1 mm size and 256 voxels for all directions
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...
>
>  mri_add_xform_to_header -c 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
>  
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>
> INFO: extension is mgz
> #
> #@# Talairach Thu Mar  3 11:35:59 GMT 2016
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
> --no-rescale --i orig.mgz --o orig_nu.mgz
>
> Linux nig05.nig.ioppn.kcl.ac.uk  
> 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 
> x86_64 x86_64 GNU/Linux
>
> recon-all -s PD1 exited with ERRORS at Thu Mar  3 11:36:02 GMT 2016
>
>
> Many Thanks
>
> With Best Wishes
>
> Flavia
>
>
>
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mris_anatomical_stats -th3

[Douglas N Greve]

/*!
   \fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
   \brief Compute vertex-wise volume based on dividing each obliquely 
truncated
   trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's
   srf2vol matlab script.
   \params w is white surface, p is pial. Output is an MRI struct of 
size nvertices
  */




On 03/06/2016 02:53 PM, Kaiming Yin wrote:
> Dear guys,
>
> I checked one of my subjects file /stats/lh.aparc.stats, in which it 
> said the commandline as:
>
> mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f 
> ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c 
> ../label/aparc.annot.ctab subject1 lh white
>
> what does the flag "-th3" mean? I'm using Freesurfer v6.0 beta.
>
> Thanks,
> Kaiming
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] group analysis all measures same results

[Douglas N Greve]

what are your command lines?

On 03/04/2016 09:01 PM, Kaiming Yin wrote:
> Dear guys,
>
> I was doing group analysis (command-line) on two groups (patients and 
> control, no age or other information). The data has been "qcached", 
> and after following the three steps as "mris_preproc, mri_glmfit and 
> mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I 
> obtained the difference on thickness in both left and right 
> hemispheres, which seems great. However, when I repeated the above 
> steps on other measures, e.g. area, area.pial, volume (also replaced 
> the parts of "thickness" in the command lines), the results seemed to 
> be exactly the same again as those in the thickness comparison, even 
> the p-value numbers in the file "cache.th40.neg.sig.cluster.summary" 
> were the same. I was using Freesurfer v6.0-beta, and I performed the 
> individual data analysis on a linux cluster and I copied/downloaded 
> the whole "qcached" subject directory to my linux laptop to perform 
> the group comparison, both using the same version of Freesurfer, does 
> it matter? Or do you know why it happened like this?
>
> Thanks,
> Kaiming
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Cortical thickness last step

[Douglas N Greve]

The code that does this is hard-coded and hard for me to follow 
(eventhough I wrote it:). It might be faster to to try to change 
ROI5.mgh. How did you create 
*/media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh?*

On 03/04/2016 04:31 PM, Sahil Bajaj wrote:
>
> Hello again,
>
>
> To calculate cortical thickness, I am running step-4 & 5 following the 
> instructions from 
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>
>
> So running step 4:
>
> *mri_surf2surf --s S01_LP --trgsubject fsaverage --hemi lh --sval 
> lh.thickness --tval lh.thickness.fsaverage.mgh --reshape*
>
> where S01_LP is my subject ID, it runs as follow:
>
>
> srcsubject = S01_LP
> srcval = lh.thickness
> srctype=
> trgsubject = fsaverage
> trgval = lh.thickness.fsaverage.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= lh
> trghemi= lh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /media/Storage/FTD_Data/S01_LP/surf/lh.sphere.reg
> Loading source data
> Reading target surface reg 
> /media/Storage/FTD_Data/fsaverage/surf/lh.sphere.reg
> Done
> Mapping Source Volume onto Source Subject Surface
> surf2surf_nnfr: building source hash (res=16).
> Surf2Surf: Forward Loop (163842)
> surf2surf_nnfr: building target hash (res=16).
> Surf2Surf: Reverse Loop (98973)
> Reverse Loop had 7939 hits
> Surf2Surf: Dividing by number of hits (163842)
> INFO: nSrcLost = 0
> nTrg121 = 157350, nTrgMulti =  6492, MnTrgMultiHits = 2.22289
> nSrc121 = 49582, nSrcLost = 0, nSrcMulti = 49391, MnSrcMultiHits = 
> 2.47411
> Saving target data
> Reshaping 6 (nvertices = 163842)
> Saving to lh.thickness.fsaverage.mgh
>
>
> Next when I run step 5 as follow:
>
> *mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh 
> --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt*
>
> It runs as follows:
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
> cwd
> cmdline mri_segstats --seg 
> /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in 
> lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt
> sysname  Linux
> hostname degas
> machine  x86_64
> user sahil
> UseRobust  0
> Loading /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh
> Loading lh.thickness.fsaverage.mgh
> ERROR: dimension mismatch between input volume and seg
>   input 27307 1 6
>   seg   23406 1 7
>
>
> As mentioned in the instructions I also tried using --reshape-factor 7 
> in step 4 also but still I get exactly same error after running step 
> 5. Could you please help me in figuring out this problem?
>
> Thanks,
> Sahil
> -- 
> -
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> Office: 713-363-9003
> E-mail:sahil.ne...@gmail.com 
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mean thickness

[Douglas N Greve]

the table file lh.aparc.thickness.table should be an ascii file. when you look 
at it with cat/more/less, what do you see? Can you send that table file?



On 03/07/2016 04:33 AM, Caroline Beelen wrote:
> Hi Bruce,
>
> I'm a beginner in FS, so I just followed tutorial instructions for generating 
> the files carefully...
> I generated it by typing in for instance (after recon-all process was done): 
> aparcstats2table --hemi lh --meas thickness --subjects A01_T1 A02_T1 etc... 
> A10_T1 --tablefile lh.aparc.thickness.table followed by the command: gnumeric 
> lh.aparc.thickness.table
>
> It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770 CPU @ 
> 3.4GHz x 8)
>
> Attached the log file (A09).
>
> Thank you very much!
>
> Greetings, Caroline
>
> -Oorspronkelijk bericht-
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
> Verzonden: zondag 6 maart 2016 16:14
> Aan: Freesurfer support list 
> Onderwerp: Re: [Freesurfer] mean thickness
>
> Hi Caroline
>
> how  did you generate the Gnumeric file? And what operating system/hardware 
> are you using? Also, please send us the recon-all.log for one of the subjects 
> that you see this happening
>
> cheers
> Bruce
>
> On Fri, 4 Mar 2016,
> Caroline Beelen wrote:
>
>> Dear Freesurfer team,
>>
>>   
>>
>> Forgive me if this is a foolish question…
>>
>>   
>>
>> I wanted to overlook cortical thickness, area and volume measures in
>> Gnumeric file after recon-all (checking edits made). However, for
>> several subjects I noticed that the values of mean thickness (final
>> column) were calculated wrong, whereas this is not the case for their
>> independent cortical thickness values. For instance, this happened to
>> subject A09. I’m including the excel file to show the example. In the
>> gnumeric file the number for this subject was depicted as 2/4964
>> instead of 2.4 etc.. What could have went wrong?
>>
>>   
>>
>> Thank you for your answer in advance.
>>
>>   
>>
>> Kind regards, Caroline
>>
>>
>>
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Embed vol geom in surf file

[WOODMAN Michael]

It isn't recognized:

$ mris_convert --vol-geom mri/T1.mgz ../fsaverage5/surf/lh.pial.tvb.bad 
surf/lh.pial.bad
unknown option --vol-geom

I can stick with the dev version if no command line utility is available for 
this in the stable version.

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Douglas N Greve 

Envoyé : mardi 8 mars 2016 00:08
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] Embed vol geom in surf file

Try mris_convert with --vol-geom option

On 03/07/2016 02:34 PM, dgw wrote:
> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?
>
> d
>
> On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman
>  wrote:
>> hi
>>
>> Is it possible to embed a volume geometry in a surface file explicitly?
>> I'm unable to find a mri_ or mris_ command which seems to do this. Is
>> there any workaround via the GUI tools?
>>
>>
>> Thanks,
>> Marmaduke
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>>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] recon-all issues

[Douglas N Greve]

Are you sure the job was not killed in the middle? The recon-all.log 
file just stops without a warning or error message. Or does this happen 
repeatedly?

On 03/07/2016 03:10 PM, Julian Jäckle wrote:
> Thank you so much for the response. Unfortunately I am not so familiar 
> with freesurfer but these files do not exist: 
> transforms/talairach_with_skull.lta, brainmask.auto.mgz, 
> brainmask.mgz. I don’t know if it is helpful but below I listed all 
> files which can be found in the subjects directory
>
> _Touch_: talairach.touch, conform.touch
>
>
> _Scripts_: recon-all-status.log, recon-all.log, recon-all.local-copy, 
> recon-all.env.bak, recon-all.env, recon-all.cmd, IsRunning.Ih+rh, 
> csurfdir, build-stamp.txt
>
>
> _Mri_: rawavg.mgz, orig_nu.mgz, orig_nu.log, orig.mgz, 
> mri_nu_correct.mni.log.bak, mri_nu_correct.mni.log
>
>-_Transforms_: 
> talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt, 
> talairach_avi_QA.log, talairach_avi.log, talairach.xfm, talairach.auto.xfm
>
> -_Orig_: 001.mgz
>
> -_tmp.mri_nu_correct.mni.12786_: sum.junk, pre-scale.mnc, 
> output.mean.dat, ones.mgz, nu2.mnc, nu2.imp, input.mean.dat
>
>  - 0: template.mnc, nu1_temp.mnc, nu1_residue.mnc, 
> nu1_mask.mnc, nu1_log.mnc, nu1_field.mnc, nu1_est.sharp, 
> nu1_est.mnc.temp, nu1_est.mnc, nu1_est.hist, nu1_corr.mnc, nu0.mnc, 
> field_volume.mnc
>
>  - 1: template.mnc, nu2_temp.mnc, nu2_residue.mnc, 
> nu2_mask.mnc, nu2_log.mnc, nu2_field.mnc, nu2_est.sharp, 
> nu2_est.mnc.temp, nu2_est.mnc, nu2_est.hist, nu2_corr.mnc, nu1.mnc, 
> field_volume.mnc
>
> (all the other subfolders are empty)
>
>
> Greetings
>
> Julian
>
>
> 2016-03-07 20:28 GMT+01:00 Bruce Fischl  >:
>
> Hi Julian
>
> can you give us more details about what exactly is missing?
>
> cheers
> Bruce
>
> On Mon, 7 Mar 2016, Julian Jäckle wrote:
>
>
> Dear FS-team
>
>
> For purposes of measuring cortical thickness I’ve been running
> recon-all as described on your RecommendedReconstruction site.
> However I am missing some files including e.g the
> skullstripped file. Could you check my log file for the root
> cause?
>
>
> Greetings
>
>
> Julian
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Embed vol geom in surf file

[Douglas N Greve]

Try mris_convert with --vol-geom option

On 03/07/2016 02:34 PM, dgw wrote:
> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?
>
> d
>
> On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman
>  wrote:
>> hi
>>
>> Is it possible to embed a volume geometry in a surface file explicitly?
>> I'm unable to find a mri_ or mris_ command which seems to do this. Is
>> there any workaround via the GUI tools?
>>
>>
>> Thanks,
>> Marmaduke
>> ___
>> 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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>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Embed vol geom in surf file

[Bruce Fischl]

I mean that the mri_surface structure and the file format it uses both 
allow a vox2ras transform to be stored. I guess the matlab code doesn't 
support it, but it could be modified to do so if anyone was interested
Bruce
On 
Mon, 7 Mar 2016, WOODMAN Michael wrote:

> sorry to bother, but can you elaborate? mris_convert --help doesn't show 
> anything.
> 
> De : freesurfer-boun...@nmr.mgh.harvard.edu 
>  de la part de Bruce Fischl 
> 
>
>
> the surface files do support embedding a ras2vox transform in them
>
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>
>
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Re: [Freesurfer] Embed vol geom in surf file

[WOODMAN Michael]

sorry to bother, but can you elaborate? mris_convert --help doesn't show 
anything.

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Bruce Fischl 



the surface files do support embedding a ras2vox transform in them

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[Freesurfer] error - mri_nu_correct.mni

[Flavia Niccolini new]

Hello,

I was wondering whether you could help with this error:

#
#@# MotionCor Thu Mar  3 11:35:51 GMT 2016
Found 1 runs
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 

/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1

 mri_convert 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz --conform 

mri_convert /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (-0, -0, 1)
Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...

 mri_add_xform_to_header -c 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 

INFO: extension is mgz
#
#@# Talairach Thu Mar  3 11:35:59 GMT 2016
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz 

Linux nig05.nig.ioppn.kcl.ac.uk 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 
14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s PD1 exited with ERRORS at Thu Mar  3 11:36:02 GMT 2016


Many Thanks

With Best Wishes

Flavia




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Re: [Freesurfer] TRACULA messy tracts

[Jacek Manko]

Dear Anastasia,

Thank you! Wouldn't you mind for example sending me these tables? As far as I 
am concerned I need only one table for all my subjects, so that would help me a 
lot. The issue with flipped coordinates in the gradient table is, as I 
mentioned before, due to the fact that I obtained these values from motion 
corrected nifti data (which I was futilely trying to preprocess as well). 
Anyway, I would like to get back to to you with that issue later on.

Best,
Jacek

Dnia 7-03-2016 o godz. 17:58 Anastasia Yendiki napisał(a):
> Hi Jacek - I looked at the data that you uploaded. The problem is that
> both the b-value table and the gradient table that you were using were
> assuming that the b=0 images were interspersed throughout your scan, when
> in fact based on your dicoms they are all in the begining of the scan. So
> the 10 entries of 0.000 need to be in the beginning of the b-value table,
> not one every 7th image. Same with the gradient table. The gradient table
> also had some flipped coordinates that would cause a different problem
> down the line.
> 
> I was able to get the right tables by using mri_convert from the
> development version of freesurfer. The 5.3 version doesn't have the
> capability to read these tables from the dicoms but the 6.0 version will.
> In the meantime you can download the dev version and use mri_convert from
> that version.
> 
> Best,
> 
> a.y
> 
> On Sun, 14 Feb 2016, Jacek Manko wrote:
> 
> > 
> > Dear Freesurfer experts,
> > 
> >  
> > 
> > I have also noticed something wrong with the tracts I reconctructed. 
> There were no erroors during the processing, but when I visualized all 
> tracts in
> > Freeview according to your command "freeview -tv 
> my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit 
> odd to say the least. Please
> > have a look at the attached image.
> > 
> >  
> > 
> > I have also notice abnormal volumes of these tracts in comparison to 
> your elmo-subjects. For example the volume of left uncinate for your 
> tutorial
> > subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy 
> seems to coincide with with what you can spot in my screen, because it 
> was my
> > first impression that these tracts are extremely large.
> > 
> >  
> > 
> > I run tracula with default commands as you stated in your tutorial, no 
> major changes were made. If there is anything you could advise me, I 
> will very
> > grateful. Are these results ok or I should udertake some steps? If you 
> perhaps need some additional information I will be pleased to provide 
> you with
> > that as well.
> > 
> >  
> > 
> > Cheers,
> > 
> > Jacek
> > 
> >  
> > 
> >  
> > 
> > Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):
> >
> >   Dear Anastasia and Tracula users,
> >  
> > I succesfully ran the longitudinal Tracula procedure for one subject. 
> However, when I visualized the tracts, they look a bit weird (not 
> smooth).
> > Even if I played with the threshold on freeview, I couldn't make them 
> look nice as in the wiki page. I checked the registration and it looks
> > accurate, so I am not sure what could be wrong. I am attaching the messy 
> looking tracts for your reference.
> >  
> > Could you tell me if I should run again with reinit=1 for these tracts?
> >  
> > Thank you very much for your time.
> > Best regards,
> >  
> >  
> > --
> > D.
> > 
> > 
> > 
> > 
> > 
> >



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Re: [Freesurfer] recon-all issues

[Julian Jäckle]

Thank you so much for the response. Unfortunately I am not so familiar with
freesurfer but these files do not exist: transforms/talairach_with_skull.lta,
brainmask.auto.mgz, brainmask.mgz. I don’t know if it is helpful but below
I listed all files which can be found in the subjects directory

*Touch*: talairach.touch, conform.touch


*Scripts*: recon-all-status.log, recon-all.log, recon-all.local-copy,
recon-all.env.bak, recon-all.env, recon-all.cmd, IsRunning.Ih+rh, csurfdir,
build-stamp.txt


*Mri*: rawavg.mgz, orig_nu.mgz, orig_nu.log, orig.mgz,
mri_nu_correct.mni.log.bak, mri_nu_correct.mni.log

   - *Transforms*:
talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt,
talairach_avi_QA.log, talairach_avi.log, talairach.xfm, talairach.auto.xfm

   -  *Orig*: 001.mgz

   -  *tmp.mri_nu_correct.mni.12786*: sum.junk, pre-scale.mnc,
output.mean.dat, ones.mgz, nu2.mnc, nu2.imp, input.mean.dat

 - 0: template.mnc, nu1_temp.mnc, nu1_residue.mnc,
nu1_mask.mnc, nu1_log.mnc, nu1_field.mnc, nu1_est.sharp, nu1_est.mnc.temp,
nu1_est.mnc, nu1_est.hist, nu1_corr.mnc, nu0.mnc,
field_volume.mnc

 - 1: template.mnc, nu2_temp.mnc, nu2_residue.mnc,
nu2_mask.mnc, nu2_log.mnc, nu2_field.mnc, nu2_est.sharp, nu2_est.mnc.temp,
nu2_est.mnc, nu2_est.hist,   nu2_corr.mnc, nu1.mnc,
field_volume.mnc

(all the other subfolders are empty)


Greetings

Julian

2016-03-07 20:28 GMT+01:00 Bruce Fischl :

> Hi Julian
>
> can you give us more details about what exactly is missing?
>
> cheers
> Bruce
>
> On Mon, 7 Mar 2016, Julian Jäckle wrote:
>
>
>> Dear FS-team
>>
>>
>> For purposes of measuring cortical thickness I’ve been running recon-all
>> as described on your RecommendedReconstruction site.
>> However I am missing some files including e.g the skullstripped file.
>> Could you check my log file for the root cause?
>>
>>
>> Greetings
>>
>>
>> Julian
>>
>>
>>
>>
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Re: [Freesurfer] Embed vol geom in surf file

[marmaduke woodman]

On 03/07/2016 08:34 PM, dgw wrote:
> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?

I wish to approximate the effect of the  --tval-xyz vol  argument to 
mris_surf2surf in the dev version, which is not present in the stable 
version, where --tval-xyz is just a flag taking no arguments.

thanks,
Marmaduke
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Re: [Freesurfer] Embed vol geom in surf file

[Bruce Fischl]

the surface files do support embedding a ras2vox transform in them

On Mon, 7 Mar 2016, dgw 
wrote:

> Marmaduke,
>
> Could you describe what it is you want to do? What do you mean by
> volume geometry? What type of information do you want to put on the
> surface?
>
> d
>
> On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman
>  wrote:
>> hi
>>
>> Is it possible to embed a volume geometry in a surface file explicitly?
>> I'm unable to find a mri_ or mris_ command which seems to do this. Is
>> there any workaround via the GUI tools?
>>
>>
>> Thanks,
>> Marmaduke
>> ___
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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
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>> properly
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>>
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Re: [Freesurfer] Embed vol geom in surf file

[dgw]

Marmaduke,

Could you describe what it is you want to do? What do you mean by
volume geometry? What type of information do you want to put on the
surface?

d

On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman
 wrote:
> hi
>
> Is it possible to embed a volume geometry in a surface file explicitly?
> I'm unable to find a mri_ or mris_ command which seems to do this. Is
> there any workaround via the GUI tools?
>
>
> Thanks,
> Marmaduke
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[Freesurfer] Embed vol geom in surf file

[marmaduke woodman]

hi

Is it possible to embed a volume geometry in a surface file explicitly? 
I'm unable to find a mri_ or mris_ command which seems to do this. Is 
there any workaround via the GUI tools?


Thanks,
Marmaduke
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Re: [Freesurfer] recon-all issues

[Bruce Fischl]

Hi Julian

can you give us more details about what exactly is missing?

cheers
Bruce
On Mon, 7 Mar 
2016, Julian Jäckle wrote:




Dear FS-team


For purposes of measuring cortical thickness I’ve been running recon-all as 
described on your RecommendedReconstruction site.
However I am missing some files including e.g the skullstripped file. Could you 
check my log file for the root cause?


Greetings


Julian



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[Freesurfer] recon-all issues

[Julian Jäckle]

Dear FS-team


For purposes of measuring cortical thickness I’ve been running recon-all as
described on your RecommendedReconstruction site. However I am missing some
files including e.g the skullstripped file. Could you check my log file for
the root cause?


Greetings


Julian


recon-all.log
Description: Binary data
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Re: [Freesurfer] Tracula bedpostx error

[Anastasia Yendiki]

Hi Prad - I'm guessing the tutorial was generated with an earlier version 
of bedpostx, tracula, or a combination of both. So I wouldn't expect to 
find the exact same values. As long as things run and the files are 
generated, it looks like you're fine.

Best,

a.y

On Mon, 7 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:

> Hi Anastasia,
>
> Thank you for clarifying that. I have a follow up question.
>
> To avoid this error while running the ball and stick model fit( Syntax error: 
> "(" unexpected), I ran it locally using "bedpostx $path_to_dmri". 
>
> The results of the overall path statistics differ from those in the tutorial. 
> I've attached my results for the left ILF (pathstats.overall_redone.txt) and 
> the tutorial results (pathstats.overall_original.txt)
>
> Is this difference due to running them on different machines or is because I 
> had to run the bedpostx command directly ?
>
> Thanks!
> -Prad
> ___
>
> _
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: Monday, March 7, 2016 10:19 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula bedpostx error
>
> Hi Prad - What will affect the speed is whether you run it locally on your
> computer (in which case it'll process one slice after the other) or on a
> cluster (in which case all the slices will be processed in parallel on
> different nodes of the cluster). This is the case regardless of the
> version that you use.
>
> Best,
>
> a.y
>
> On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
>
>>
>>
>> Hello Anastasia,
>>
>> I have been trying to run through the tutorial with one of the subjects from 
>> the tutorial(elmo.2008) to familiarize myself with Tracula.
>> The preprocessing step seems to have been completed without any errors (Log 
>> file attached).However, when I proceed with the ball and stick model fit
>> step, I get the following error
>>
>> bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
>> /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: 
>> Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu
>> 12.04 with FSL 5.0.9.
>>
>> In an earlier post where the same error was 
>> encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
>>  you recommended
>> running bedpostx directly.
>>
>> Would this impact the results or run time in any way? and is there something 
>> I can do to fix this error if it is likely to take much longer?
>>
>>
>> Thanks!
>>
>> -Prad
>>
>>
>>
>>
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Re: [Freesurfer] Tracula bedpostx error

[Bharadwaj, Pradyumna - (prad)]

Hi Anastasia,

Thank you for clarifying that. I have a follow up question.

To avoid this error while running the ball and stick model fit( Syntax error: 
"(" unexpected), I ran it locally using "bedpostx $path_to_dmri". 

The results of the overall path statistics differ from those in the tutorial. 
I've attached my results for the left ILF (pathstats.overall_redone.txt) and 
the tutorial results (pathstats.overall_original.txt)

Is this difference due to running them on different machines or is because I 
had to run the bedpostx command directly ?

Thanks!
-Prad
___

_
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Anastasia Yendiki 

Sent: Monday, March 7, 2016 10:19 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula bedpostx error

Hi Prad - What will affect the speed is whether you run it locally on your
computer (in which case it'll process one slice after the other) or on a
cluster (in which case all the slices will be processed in parallel on
different nodes of the cluster). This is the case regardless of the
version that you use.

Best,

a.y

On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:

>
>
> Hello Anastasia,
>
> I have been trying to run through the tutorial with one of the subjects from 
> the tutorial(elmo.2008) to familiarize myself with Tracula.
> The preprocessing step seems to have been completed without any errors (Log 
> file attached).However, when I proceed with the ball and stick model fit
> step, I get the following error
>
> bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
> /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: 
> Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu
> 12.04 with FSL 5.0.9.
>
> In an earlier post where the same error was 
> encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
>  you recommended
> running bedpostx directly.
>
> Would this impact the results or run time in any way? and is there something 
> I can do to fix this error if it is likely to take much longer?
>
>
> Thanks!
>
> -Prad
>
>
>
>
# Title Pathway Statistics
#
# generating_program /usr/local/freesurfer/dev/bin/dmri_pathstats
# cvs_version 
# cmdline /usr/local/freesurfer/dev/bin/dmri_pathstats --intrc 
/space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr
 --dtbase /space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dmri/dtifit 
--path lh.ilf --subj elmo.2008 --out 
/space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
 --outvox 
/space/freesurfer/subjects/diffusion_tutorial/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt
 
# sysname Linux
# hostname compute-0-29
# machine x86_64
# user ayendiki
# anatomy_type pathway
#
# subjectname elmo.2008
# pathwayname lh.ilf
#
Count 1500
Volume 902
Len_Min 36
Len_Max 83
Len_Avg 53.2167
Len_Center 54
AD_Avg 0.00137149
AD_Avg_Weight 0.00137135
AD_Avg_Center 0.00132052
RD_Avg 0.000618602
RD_Avg_Weight 0.000615934
RD_Avg_Center 0.000625125
MD_Avg 0.000869563
MD_Avg_Weight 0.000867741
MD_Avg_Center 0.000856922
FA_Avg 0.482952
FA_Avg_Weight 0.484575
FA_Avg_Center 0.453493
# Title Pathway Statistics
#
# generating_program /apps/freesurfer/bin/dmri_pathstats
# cvs_version 
# cmdline /apps/freesurfer/bin/dmri_pathstats --intrc 
/home/biba1/testing_tracula/diffusion/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr 
--dtbase /home/biba1/testing_tracula/diffusion/elmo.2008/dmri/dtifit --path 
lh.ilf --subj elmo.2008 --out 
/home/biba1/testing_tracula/diffusion/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt
 --outvox 
/home/biba1/testing_tracula/diffusion/elmo.2008/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt
 
# sysname Linux
# hostname BIBAStation1
# machine x86_64
# user biba1
# anatomy_type pathway
#
# subjectname elmo.2008
# pathwayname lh.ilf
#
Count 1500
Volume 1261
Len_Min 33
Len_Max 86
Len_Avg 56.282
Len_Center 59
AD_Avg 0.00133899
AD_Avg_Weight 0.00133384
AD_Avg_Center 0.0013349
RD_Avg 0.000625518
RD_Avg_Weight 0.000628174
RD_Avg_Center 0.000615722
MD_Avg 0.000863341
MD_Avg_Weight 0.000863395
MD_Avg_Center 0.000855447
FA_Avg 0.463227
FA_Avg_Weight 0.459711
FA_Avg_Center 0.467562
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Re: [Freesurfer] path.pd.trk format

[Anastasia Yendiki]

Anatorig will take you to freesurfer space. I's suggest smoothing these to 
make them more presentable, and potentially also thresholding them based 
on the probability map (which is the sum of these streamlines).

On Mon, 7 Mar 2016, Peled, Noam wrote:

> I want to display it in my new 3d visualization tool, along the hemispheres 
> and the subcortical regions.
> The hemispheres and the subcortical regions I import from freesurfer.
>
> Thanks,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, March 07, 2016 12:20 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> What to you want to display it on? If you want to display in on the FA
> map, or anything that's in diffusion space, you don't need any transform.
>
> On Mon, 7 Mar 2016, Peled, Noam wrote:
>
>> So for plotting the fibers, like in freeview, should I just use the 
>> /dmri/xfms/diff2anatorig..mat or 
>> /dmri/xfms/diff2anat..mat transformation matrices?
>>
>> Thanks again,
>> Noam
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Monday, March 07, 2016 12:09 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] path.pd.trk format
>>
>> Yes, native diffusion space.
>>
>> On Mon, 7 Mar 2016, Peled, Noam wrote:
>>
>>> Thanks!
>>> Do you in which space are the voxel coordinates coordinates? Are they in 
>>> the diffusion space?
>>>
>>> Thanks again,
>>> Noam
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>>> [ayend...@nmr.mgh.harvard.edu]
>>> Sent: Saturday, March 05, 2016 5:10 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] path.pd.trk format
>>>
>>> Hi Noam - You can read the .trk file with trackvis. It contains all the
>>> path samples that are added up to created the probability distribution of
>>> the path. Please keep in mind, however, that this .trk file is just meant
>>> for generating stats and not for visualization, so these are not the usual
>>> smoothed kind of streamlines that you get from deterministic tractography.
>>> It contains only integer voxel coordinates, so the streamlines will look
>>> sort of like step ladders if you visualize them.
>>>
>>> Best,
>>>
>>> a.y
>>>
>>> On Tue, 16 Feb 2016, Peled, Noam wrote:
>>>
 Hello,
 I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
 output directory.
 How can I read this file? I would like to read the actual splines and not 
 the probabilistic distribution in path.pd.nii.gz.

 Thanks,
 Noam Peled


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>>>
>>>
>>>
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>>
>>
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Re: [Freesurfer] path.pd.trk format

[Peled, Noam]

I want to display it in my new 3d visualization tool, along the hemispheres and 
the subcortical regions.
The hemispheres and the subcortical regions I import from freesurfer.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Monday, March 07, 2016 12:20 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] path.pd.trk format

What to you want to display it on? If you want to display in on the FA
map, or anything that's in diffusion space, you don't need any transform.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> So for plotting the fibers, like in freeview, should I just use the 
> /dmri/xfms/diff2anatorig..mat or 
> /dmri/xfms/diff2anat..mat transformation matrices?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, March 07, 2016 12:09 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Yes, native diffusion space.
>
> On Mon, 7 Mar 2016, Peled, Noam wrote:
>
>> Thanks!
>> Do you in which space are the voxel coordinates coordinates? Are they in the 
>> diffusion space?
>>
>> Thanks again,
>> Noam
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Saturday, March 05, 2016 5:10 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] path.pd.trk format
>>
>> Hi Noam - You can read the .trk file with trackvis. It contains all the
>> path samples that are added up to created the probability distribution of
>> the path. Please keep in mind, however, that this .trk file is just meant
>> for generating stats and not for visualization, so these are not the usual
>> smoothed kind of streamlines that you get from deterministic tractography.
>> It contains only integer voxel coordinates, so the streamlines will look
>> sort of like step ladders if you visualize them.
>>
>> Best,
>>
>> a.y
>>
>> On Tue, 16 Feb 2016, Peled, Noam wrote:
>>
>>> Hello,
>>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>>> output directory.
>>> How can I read this file? I would like to read the actual splines and not 
>>> the probabilistic distribution in path.pd.nii.gz.
>>>
>>> Thanks,
>>> Noam Peled
>>>
>>>
>> ___
>> Freesurfer mailing list
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>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
> ___
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>
>
>
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Re: [Freesurfer] T2pial shrinks pial surface

[Bruce Fischl]

Hi Chris

I took a look,  and the problem is that there are big changes in contrast 
between occipital and frontal lobes. If we normalize both posterior and 
frontal wm to 110, occipital gray matter gets mapped to 180 but frontal 
gray gets >255. This kind of thing can be caused by a transmit "bias" 
field, or by dielectric effects.  I'm not sure why this is a problem with 
this dataset and not others


cheers
Bruce

On Mon, 7 Mar 2016, Chris Adamson wrote:


Thanks Bruce.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson
Sent: Monday, 7 March 2016 1:54 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

It is checkT2pial.zip

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, 7 March 2016 1:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Mon, 7 Mar
2016, Chris Adamson wrote:


How can I upload it to you?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Monday, 7 March 2016 1:25 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

Hi Chris

if you upload that dataset I'll try to take a look soon

cheers
Bruce


On Mon, 7 Mar 2016, Chris Adamson wrote:



The T2pial option mostly works beautifully. I have a few cases where
the pial surface just shrinks globally and wraps over the white
surface (see attached). I have checked the T2.mgz and the
registration with the T1 is fine. This happens sometimes in one hemisphere only.

Any ideas?

 

[IMAGE]

Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au

 

[IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]

 

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Re: [Freesurfer] path.pd.trk format

[Anastasia Yendiki]

What to you want to display it on? If you want to display in on the FA 
map, or anything that's in diffusion space, you don't need any transform.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> So for plotting the fibers, like in freeview, should I just use the 
> /dmri/xfms/diff2anatorig..mat or 
> /dmri/xfms/diff2anat..mat transformation matrices?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, March 07, 2016 12:09 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Yes, native diffusion space.
>
> On Mon, 7 Mar 2016, Peled, Noam wrote:
>
>> Thanks!
>> Do you in which space are the voxel coordinates coordinates? Are they in the 
>> diffusion space?
>>
>> Thanks again,
>> Noam
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Saturday, March 05, 2016 5:10 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] path.pd.trk format
>>
>> Hi Noam - You can read the .trk file with trackvis. It contains all the
>> path samples that are added up to created the probability distribution of
>> the path. Please keep in mind, however, that this .trk file is just meant
>> for generating stats and not for visualization, so these are not the usual
>> smoothed kind of streamlines that you get from deterministic tractography.
>> It contains only integer voxel coordinates, so the streamlines will look
>> sort of like step ladders if you visualize them.
>>
>> Best,
>>
>> a.y
>>
>> On Tue, 16 Feb 2016, Peled, Noam wrote:
>>
>>> Hello,
>>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>>> output directory.
>>> How can I read this file? I would like to read the actual splines and not 
>>> the probabilistic distribution in path.pd.nii.gz.
>>>
>>> Thanks,
>>> Noam Peled
>>>
>>>
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Re: [Freesurfer] Tracula bedpostx error

[Anastasia Yendiki]

Hi Prad - What will affect the speed is whether you run it locally on your 
computer (in which case it'll process one slice after the other) or on a 
cluster (in which case all the slices will be processed in parallel on 
different nodes of the cluster). This is the case regardless of the 
version that you use.


Best,

a.y

On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:




Hello Anastasia,

I have been trying to run through the tutorial with one of the subjects from 
the tutorial(elmo.2008) to familiarize myself with Tracula.
The preprocessing step seems to have been completed without any errors (Log 
file attached).However, when I proceed with the ball and stick model fit
step, I get the following error

bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri
/apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: 
"(" unexpected. I'm running the tutorial locally on Ubuntu
12.04 with FSL 5.0.9.

In an earlier post where the same error was 
encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html)
 you recommended
running bedpostx directly.

Would this impact the results or run time in any way? and is there something I 
can do to fix this error if it is likely to take much longer?


Thanks!

-Prad



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Re: [Freesurfer] path.pd.trk format

[Peled, Noam]

So for plotting the fibers, like in freeview, should I just use the 
/dmri/xfms/diff2anatorig..mat or 
/dmri/xfms/diff2anat..mat transformation matrices?

Thanks again,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Monday, March 07, 2016 12:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] path.pd.trk format

Yes, native diffusion space.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> Thanks!
> Do you in which space are the voxel coordinates coordinates? Are they in the 
> diffusion space?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Saturday, March 05, 2016 5:10 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Hi Noam - You can read the .trk file with trackvis. It contains all the
> path samples that are added up to created the probability distribution of
> the path. Please keep in mind, however, that this .trk file is just meant
> for generating stats and not for visualization, so these are not the usual
> smoothed kind of streamlines that you get from deterministic tractography.
> It contains only integer voxel coordinates, so the streamlines will look
> sort of like step ladders if you visualize them.
>
> Best,
>
> a.y
>
> On Tue, 16 Feb 2016, Peled, Noam wrote:
>
>> Hello,
>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>> output directory.
>> How can I read this file? I would like to read the actual splines and not 
>> the probabilistic distribution in path.pd.nii.gz.
>>
>> Thanks,
>> Noam Peled
>>
>>
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>
>
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Re: [Freesurfer] path.pd.trk format

[Anastasia Yendiki]

Yes, native diffusion space.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> Thanks!
> Do you in which space are the voxel coordinates coordinates? Are they in the 
> diffusion space?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Saturday, March 05, 2016 5:10 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Hi Noam - You can read the .trk file with trackvis. It contains all the
> path samples that are added up to created the probability distribution of
> the path. Please keep in mind, however, that this .trk file is just meant
> for generating stats and not for visualization, so these are not the usual
> smoothed kind of streamlines that you get from deterministic tractography.
> It contains only integer voxel coordinates, so the streamlines will look
> sort of like step ladders if you visualize them.
>
> Best,
>
> a.y
>
> On Tue, 16 Feb 2016, Peled, Noam wrote:
>
>> Hello,
>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>> output directory.
>> How can I read this file? I would like to read the actual splines and not 
>> the probabilistic distribution in path.pd.nii.gz.
>>
>> Thanks,
>> Noam Peled
>>
>>
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Re: [Freesurfer] TRACULA messy tracts

[Anastasia Yendiki]

Hi Jacek - I looked at the data that you uploaded. The problem is that 
both the b-value table and the gradient table that you were using were 
assuming that the b=0 images were interspersed throughout your scan, when 
in fact based on your dicoms they are all in the begining of the scan. So 
the 10 entries of 0.000 need to be in the beginning of the b-value table, 
not one every 7th image. Same with the gradient table. The gradient table 
also had some flipped coordinates that would cause a different problem 
down the line.


I was able to get the right tables by using mri_convert from the 
development version of freesurfer. The 5.3 version doesn't have the 
capability to read these tables from the dicoms but the 6.0 version will. 
In the meantime you can download the dev version and use mri_convert from 
that version.


Best,

a.y

On Sun, 14 Feb 2016, Jacek Manko wrote:



Dear Freesurfer experts,

 

I have also noticed something wrong with the tracts I reconctructed. There were 
no erroors during the processing, but when I visualized all tracts in
Freeview according to your command "freeview -tv 
my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit odd to say 
the least. Please
have a look at the attached image.

 

I have also notice abnormal volumes of these tracts in comparison to your 
elmo-subjects. For example the volume of left uncinate for your tutorial
subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy seems 
to coincide with with what you can spot in my screen, because it was my
first impression that these tracts are extremely large.

 

I run tracula with default commands as you stated in your tutorial, no major 
changes were made. If there is anything you could advise me, I will very
grateful. Are these results ok or I should udertake some steps? If you perhaps 
need some additional information I will be pleased to provide you with
that as well.

 

Cheers,

Jacek

 

 

Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):

  Dear Anastasia and Tracula users,
 
I succesfully ran the longitudinal Tracula procedure for one subject. However, 
when I visualized the tracts, they look a bit weird (not smooth).
Even if I played with the threshold on freeview, I couldn't make them look nice 
as in the wiki page. I checked the registration and it looks
accurate, so I am not sure what could be wrong. I am attaching the messy 
looking tracts for your reference.
 
Could you tell me if I should run again with reinit=1 for these tracts?
 
Thank you very much for your time.
Best regards,
 
 
--
D.





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Re: [Freesurfer] Recon Reprocessing Issues

[Bruce Fischl]

I got it, thanks
Bruce
On Mon, 7 Mar 2016, Champe Barton wrote:



Hey Bruce,

I got a notification saying the email my recon-all.log file attachment was too 
large and had to await moderator approval to be posted to the support list. I 
was just wondering if you received it or if I should resend it.

Best,
Champe

Sent from my iPhone


On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:

Hi Champe

can you send us the recon-all.log file?

cheers
Bruce

On Sun, 6 Mar 2016, Champe Barton wrote:

Hi Freesurfer People,
I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I
have System Integrity Protection disabled (though I hadn’t experienced any
issues that could have been a result of that function). Everything in
FreeSurfer works fine for me—I ran recon-all and successfully processed
dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
the pial and white surfaces, and I successfully deleted unnecessary voxels
and added a set of control points (in both cases, being careful to make and
save the changes on all necessary slices with the brainmask volume
highlighted). My only issue is that when I reprocess the data using
recon-all -autorecon2-cp -autorecon3 -subjid , it runs
through the reconstruction without error and then shows no changes at all in
freeview when I view the volumes/surfaces. The deleted voxels still appear
deleted and I can still load the control points, so why wouldn’t it make the
changes?
And just to provide a little extra info: I encounter the same problem when I
reprocess the tutorial data for the pial edits tutorial. I delete the voxels
as instructed, save the file, reprocess it without error, and then nothing’s
changed when I view it all again in freeview.
Any help would be HUGELY appreciated—I’ve stressed over this for weeks
trying to get my computer to function properly so that I can begin my work
as a research assistant in a neuropsych lab editing and analyzing brain
scans with FreeSurfer.
Thanks,
Champe

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Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[Francis Tyson Thomas]

Hi Richard,

That information was a lot helpful. At this point I'm currently trying to
reduce the recon-all processing time as much as possible and for this
reason I was looking to get the -use-gpu flag working. I'm currently
running a freesurfer v6 beta version on Ubuntu 14.04.4. With regard to the
graphic card it is a dual K2200 configuration (I guess they are running in
sli configuration - although I'm not completely sure).

When you mentioned you compiled everything, I believe you were referring to
compiling CUDA 7.5 for Ubuntu 14.04. Because after seeing the link -
https://developer.nvidia.com/cuda-gpus
-  we settled for CUDA 5 since it was the compatible version mentioned for
K2200. Does that mean CUDA 7.5 is backwards compatible with a slight
tinkering and can be used with freesurfer 6.0 ?

I however tried to setup CUDA 5 following the instructions in the link -
http://www.unixmen.com/how-to-install-cuda-5-0-toolkit-in-ubuntu/ -
however, I'm not able to get it running. I keep getting the following error
"Unable to acquire CUDA device". Does this sound familiar ?

If you can share some more information in setting this up it will be great
since the amount of time recon-all takes is quite too long for running
multiple datasets. Most importantly we are concerned about the hippocampal
segmentation in freesurfer 6 rather than recon-all and so speeding this up
would be extremely helpful.

Thank you,
Tyson

On Thu, Mar 3, 2016 at 2:23 PM, R Edgar  wrote:

> On 3 March 2016 at 13:22, Francis Tyson Thomas
>  wrote:
>
> > Also, it looks like development for GPU usage has been halted for now
> and so
> > I was trying to use the CUDA 5 for getting it working under ubuntu
> 14.04. I
> > have been not successful that as the cuda device isn't getting selected.
> Do
> > you have any recommendations on that?
>
> I have recently started looking at the CUDA port again, although I'm
> making no promises as to the amount of time I'll have to spend on it.
> This said I've got mri_ca_register running with CUDA 7.5 on my
> machine. On my E3 Xeon with a K1200, I can run mri_ca_register with
> the test dataset in about 9 minutes.
>
> Are you compiling from source? I had to tamper a bit with the
> configure script before compiling CUDA was enabled again. I don't have
> access to the right machine at the moment, but as I recall, there was
> a line
> with_cuda=""
> which I had to comment out, since it was overriding the path to the
> machine's CUDA installation which I was passing on the command line.
> There are a few other minor bug fixes and performance improvements for
> GPU code which I've submitted for Zeke; no new kernels yet, I'm
> afraid.
>
> If you could give me some more details about what you're doing, I may
> be able to help.
>
> Just the standard warning: the GPU results will be different from the
> CPU results on the same inputs. We've been kicking around some ideas
> recently to quantify how different (and to devise input datasets where
> the correct answers are unambiguous).
>
> Regards,
>
> Richard
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Re: [Freesurfer] Recon Reprocessing Issues

[Champe Barton]

Hey Bruce,

I got a notification saying the email my recon-all.log file attachment was too 
large and had to await moderator approval to be posted to the support list. I 
was just wondering if you received it or if I should resend it. 

Best,
Champe

Sent from my iPhone

> On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:
> 
> Hi Champe
> 
> can you send us the recon-all.log file?
> 
> cheers
> Bruce
>> On Sun, 6 Mar 2016, Champe Barton wrote:
>> 
>> Hi Freesurfer People,
>> I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I
>> have System Integrity Protection disabled (though I hadn’t experienced any
>> issues that could have been a result of that function). Everything in
>> FreeSurfer works fine for me—I ran recon-all and successfully processed
>> dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
>> the pial and white surfaces, and I successfully deleted unnecessary voxels
>> and added a set of control points (in both cases, being careful to make and
>> save the changes on all necessary slices with the brainmask volume
>> highlighted). My only issue is that when I reprocess the data using
>> recon-all -autorecon2-cp -autorecon3 -subjid , it runs
>> through the reconstruction without error and then shows no changes at all in
>> freeview when I view the volumes/surfaces. The deleted voxels still appear
>> deleted and I can still load the control points, so why wouldn’t it make the
>> changes?
>> And just to provide a little extra info: I encounter the same problem when I
>> reprocess the tutorial data for the pial edits tutorial. I delete the voxels
>> as instructed, save the file, reprocess it without error, and then nothing’s
>> changed when I view it all again in freeview.
>> Any help would be HUGELY appreciated—I’ve stressed over this for weeks
>> trying to get my computer to function properly so that I can begin my work
>> as a research assistant in a neuropsych lab editing and analyzing brain
>> scans with FreeSurfer.
>> Thanks,
>> Champe
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[Freesurfer] Hiring: Houston, TX - Data Processing/Analysis

[Rockers, Elijah D.]

Hello,

The Nantz National Alzheimer Center, in Houston, TX is looking to fill two 
positions pertaining to neuroimaging and analysis.

Be aware that we cannot accept remote employment, the candidate would have to 
work day-to-day in the city of Houston.

Any interested person is encouraged to review the job postings, which are 
attached.
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DataAnalyist.docx
Description: DataAnalyist.docx


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Re: [Freesurfer] path.pd.trk format

[Peled, Noam]

Thanks!
Do you in which space are the voxel coordinates coordinates? Are they in the 
diffusion space? 

Thanks again,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Saturday, March 05, 2016 5:10 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] path.pd.trk format

Hi Noam - You can read the .trk file with trackvis. It contains all the
path samples that are added up to created the probability distribution of
the path. Please keep in mind, however, that this .trk file is just meant
for generating stats and not for visualization, so these are not the usual
smoothed kind of streamlines that you get from deterministic tractography.
It contains only integer voxel coordinates, so the streamlines will look
sort of like step ladders if you visualize them.

Best,

a.y

On Tue, 16 Feb 2016, Peled, Noam wrote:

> Hello,
> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
> output directory.
> How can I read this file? I would like to read the actual splines and not the 
> probabilistic distribution in path.pd.nii.gz.
>
> Thanks,
> Noam Peled
>
>
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[Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview)

[Veronica.Popescu]

Dear all, 
I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). 
The mri_convert doesn't work with no error message. which mri_convert gives 
/usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which 
exits with errors with no error message in  the log). 
I made sure all the paths are 777. I did the recommended "sudo ln -s  
libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in 
x86_64-linux-gnu. 
The same problem with freeview, nothing happens. 
The output is: 

"Mon Feb 22 18:27:05 CET 2016
/usr/local/freesurfer/subjects/myscan
/usr/local/freesurfer/bin/recon-all
-s myscan -i myscan.nii.gz
subjid myscan
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  15308 
maxlocks unlimited
maxsignal    15308 
maxmessage   819200 
maxnice  0 
maxrtprio    0 
maxrttime    unlimited

 total   used   free shared    buffers cached
Mem:   3940392    3452568 487824 223760 262988    2343920
-/+ buffers/cache: 845660    3094732
Swap:  2023420  77288    1946132


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 
2010-02-20 at 20:19:13
###
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
###
/usr/local/freesurfer/subjects/myscan

 mri_convert /usr/local/freesurfer/subjects/myscan.nii.gz 
/usr/local/freesurfer/subjects/myscan/mri/orig/001.mgz 

Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s myscan exited with ERRORS at Mon Feb 22 18:27:07 CET 2016

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting";
It creates the directory myscan but the folders myscan/mri/orig and 
myscan/mri/transforms are empty. Before running I changed the rights -R a+w for 
 /usr/local/freesurfer/subjects. 

I tried to use mri_convert myscan.nii.gz myscan.mgz and it doesn't do anything, 
no error message it just skips to a new line.
mri_convert -h or mri_convert --help also don't have any output. 
And recon-all -s bert -autorecon1 gives:

"Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwxrwx 1 root root 472994 Feb  8 16:54 
/usr/local/freesurfer/subjects/bert/scripts/recon-all.log
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /usr/local/freesurfer
    Previous: /space/freesurfer/centos4.0/stable
#
#@# MotionCor Mon Feb 22 18:24:35 CET 2016
Found 3 runs
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has  frames
Linux MSveronica 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s bert exited with ERRORS at Mon Feb 22 18:24:35 CET 2016"

If I try to run:

"freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v 
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f 
$SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f 
$SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f 
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" 
as indicated on the website nothing happens, no error message. 

Thank you in advance! 
Veronica



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Re: [Freesurfer] Medial crossing surfaces

[Bruce Fischl]

Hi Maryam

I guess, although it's hard to say without looking at your data. I think 
the upcoming V6 does much better on the midline. If you upload your 
data I can take a look. For the command line you can check out the 
recon-all help and just rerun the pial surface generation


cheers
Bruce
On Mon, 7 Mar 2016, maryam koochaki wrote:


 Hi Bruce,
I am editing aseg to correct the boundaries that excluded the lateral
ventricle. The problem with lateral ventricle has been solved after running
the process with -noaseg flag.
But the boundaries in the middle, is crossing to the other hemesphere in
some cases.

I even tried -autorecon2-cp, the problem still exists.
aparc+aseg has not been updated after running the process.

Does Celine's case apply to mine? Here is your answer to Celine:

Hi Celine
the only existing way to correct this would be to create two volumes in
addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and
rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the
contralateral hemisphere that are causing problems, then rerun
mris_make_surfaces for each hemi, using the appropriate volume. At some
point I guess we should put an intersection check into it for the contra
hemi
cheers
Bruce

Could you help me with the exact command line? 

Thank you in advance for your help,
Maryam


 








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[Freesurfer] System crash by extremely much generated output v6 beta

[Ed Gronenschild]

Hi developers,

My environment:
MacPro OSX10.7 installed on a partition of 20 GByte;
FreeSurfer v6 beta

During processing recon-all on 4 subjects in parallel
using 4 terminal windows, the 20 GByte partition got
full. This happened twice and I managed to trace down
the offending stage in the pipeline: topology fixing,
in particular the tool mris_topo_fixer.
Most probably it went into an endless iteration loop
generating so much output the disk got full.

Cheers,
Ed

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[Freesurfer] Medial crossing surfaces

[maryam koochaki]

 Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral 
ventricle. The problem with lateral ventricle has been solved after running the 
process with -noaseg flag. But the boundaries in the middle, is crossing to the 
other hemesphere in some cases.
I even tried -autorecon2-cp, the problem still exists.
aparc+aseg has not been updated after running the process.

Does Celine's case apply to mine? Here is your answer to Celine:
Hi Celine
the only existing way to correct this would be to create two volumes in 
addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and 
rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the 
contralateral hemisphere that are causing problems, then rerun 
mris_make_surfaces for each hemi, using the appropriate volume. At some 
point I guess we should put an intersection check into it for the contra 
hemicheers
Bruce
Could you help me with the exact command line? 
Thank you in advance for your help,Maryam


 






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