Re: [Freesurfer] Freesurfer 6.0?

[Douglas Greve]

We are working pretty hard to get it out but we are still reluctant to 
set a hard date. I think we'll have a beta version in two weeks, but 
that's just a guess.


doug



On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote:


Hi there

Do we have a potential date for the Freesurfer 6.0 release? I was told 
I would want to re-run all my subjects to create better surfaces using 
Freesurfer 6.0 and I am wondering if it really will improve surface 
extraction that much.


Many thanks!

Trisanna


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



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Re: [Freesurfer] Running Several Versions of fsfast GLM In Parallel Leads to "Stale File Handles"

[Douglas Greve]

Try this: on line 160 of preproc-sess, change

  if(-w .) then

to

 if(-w . && $nolog != 1)

I think that should do it.



On 7/25/16 7:53 PM, Taylor, Johnmark wrote:

Hello,

I have been trying to run several versions of the same GLM analysis, 
trying out different parameters to see if they affect the results. For 
instance, I am running the GLM with different levels of smoothing, 
per-session versus per-run motion correction, etc. To speed this up, I 
am trying to do these GLMs in parallel. However, when I do this, I run 
into a "stale file handle" problem. As near as I can tell, this occurs 
because the analyses try to read and write to the same log files at 
the same time. A typical error message is 
"/net/rcss2/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/fpoinfips01/scripts/glm/log/preproc-160718_xu_loc01_sub02-bold.log: 
Stale file handle". I have tried putting "-nolog" in the call to 
selxavg3-sess, but this doesn't prevent the creation of log files when 
it makes the sub-calls to the various pre-processing functions. Is 
there any way around this? It would be rather slow to try to run the 
GLMs sequentially, so I am wondering if anybody has figured out a way 
around this problem.


Much obliged,

JohnMark


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[Freesurfer] Running Several Versions of fsfast GLM In Parallel Leads to "Stale File Handles"

[Taylor, Johnmark]

Hello,

I have been trying to run several versions of the same GLM analysis, trying
out different parameters to see if they affect the results. For instance, I
am running the GLM with different levels of smoothing, per-session versus
per-run motion correction, etc. To speed this up, I am trying to do these
GLMs in parallel. However, when I do this, I run into a "stale file handle"
problem. As near as I can tell, this occurs because the analyses try to
read and write to the same log files at the same time. A typical error
message is
"/net/rcss2/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/fpoinfips01/scripts/glm/log/preproc-160718_xu_loc01_sub02-bold.log:
Stale file handle". I have tried putting "-nolog" in the call to
selxavg3-sess, but this doesn't prevent the creation of log files when it
makes the sub-calls to the various pre-processing functions. Is there any
way around this? It would be rather slow to try to run the GLMs
sequentially, so I am wondering if anybody has figured out a way around
this problem.

Much obliged,

JohnMark
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Re: [Freesurfer] bbregister problem in FS5.1

[Douglas Greve]

Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see. 
You can just copy mri_convert from 5.3 into 5.1 (make a backup first)



On 7/25/16 12:31 PM, Fred Sampedro wrote:

Hi Douglas,

Thank you very much for answering. Unfortunately, I can read all the 
files without any problem in FSL/SPM, and I still have more than 40GB 
of free space. In fact, running the exact same instruction in 
freesurfer 5.3 works fine.


:(



On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve 
> wrote:


It looks like one of two things:

1. The files SUBJ_ID.nii.gz is corrupted. See if another tool
(FSL, SPM, AFNI) can read the file

2. You have run out of disk space


On 7/24/16 10:52 AM, Fred Sampedro wrote:

Dear FS experts,

I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
and I'm trying to run bbregister to register a AV45-PET image to
its corresponding FS processed T1 image. For that, I'm trying to run:

bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat
--init-fsl --t1

And I keep getting segfaults:

Log file is register.dat.log
dom jul 24 16:44:19 CEST 2016

$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15
17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
./tmp.bbregister.5353/template.nii
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
./tmp.bbregister.5353/template.nii
Segmentation fault (core dumped)


I have tried the same installation and command in two different
computers and obtained the same segfault. I have also tried the
same pipeline using instead the FS version
freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the
same result. I didn't have this issue using freesurfer 5.3, but I
need to use 5.1 for an ongoing project.

I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel
Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.

Any help would be much appreciated,

Thanks a lot in advance,

Fred Sampedro


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Re: [Freesurfer] normalizing in fsgd

[Douglas Greve]

Actually, I checked the code and found that I had already put a flag in 
there to do this (I'm so clever). Add


ReScaleFlag 1

in addition to

DeMeanFlag 1




On 7/25/16 11:22 AM, Douglas Greve wrote:


No, that flag does not exist, but it is a good idea! You'll have to 
normalize them by hand.



On 7/24/16 1:33 PM, miracle ozzoude wrote:

Hello freesurfer experts,
I am trying to normalize my continuous variables in my fsgd file. Is 
this the correct term to add to my fsgd file in order for mri_glmfit 
to normalize it?


GroupDescriptorFile 1
Title PCS
Class group1
Class group2
Normalize 1
Variables Age Education Scoreone Scoretwo
Input 053 group1 47 18 3.4 5.6
Input 054 group2 50 16 5.3 2.8

Thank you,
Paul


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Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

[Nicola Toschi]

Hi Doug,

thank you - using this new version changed everything back to "normal" 
(small clusters, few results), so it may indeed have been a problem with 
that particular version.

Thanks again,

Nicola

On 7/22/2016 8:22 PM, Douglas N Greve wrote:
>
> That version may have had a bug. Try  this one
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
> btw, you should not be using the dev version of recon-all
>
> On 07/22/2016 02:01 PM, Nicola Toschi wrote:
>> Hi,
>>
>> it's a dev version downloaded on Jan 17th 2016.
>>
>> As mentioned in my other mail, I have uploaded a full glmdir at
>>
>> http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
>>
>> thanks for your time,
>>
>> Nicola
>>
>> On 7/22/2016 6:35 PM, Douglas N Greve wrote:
>>> what version does it fail on? If a dev version, when did you 
>>> download it?
>>>
>>> On 07/22/2016 12:15 PM, Nicola Toschi wrote:
 Hi Again,

  (apologies for the many posts): I should add that none of this 
 happens (and everything works fine - no warning and small clusters 
 which look reasonable) if I use version 5.3.

 Thank you,

 Nicola

 On 7/22/2016 2:10 PM, Nicola Toschi wrote:
> Hi,
>
> thanks - I tried using "abs" as well as a higher threshold, 
> however the
> large, whole-brain cluster (as well as the warning messages) still 
> remains.
>
> Do the warnings:
>
> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
> WARNING: 251446 NaNs found in volume
>
> give any clues?
>
> The strange thing is that everything is fine (small clusters and no
> warning) when I use t-tests )i.e. just the first or second line of 
> the F
> test).
>
> Thanks a lot for your time,
>
> Nicola
>
>
> On 07/21/2016 11:53 PM, Douglas N Greve wrote:
>> Try using abs instead of pos. abs (absolute) is more appropriate 
>> since
>> an F test is unsigned. Also, I would go with a threshold of 2 and 
>> not
>> 1.3. I'm just now finding out that such a low threshold can cause a
>> lot of false postives on real data.
>>
>>
>> On 07/21/2016 05:32 PM, Nicola Toschi wrote:
>>> Hi,
>>>
>>> thanks for your reply. The mri_glmfit-sim was pasted below, here it
>>> is the dereferenced version:
>>>
>>>
>>> /usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
>>> design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
>>>
>>>
>>> thanks again,
>>>
>>> Nicola
>>>
>>> On 7/21/2016 11:13 PM, Douglas N Greve wrote:
 That is the mri_glmfit command, I need the mri_glmfit-sim. Also,
 please do not include variables, just the full command with all
 dereferenced args

 On 07/21/2016 03:28 PM, Nicola Toschi wrote:
> Hi,
>
> here it is (I also pasted the mri_glmfit line):
>
> /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output 
> directory//
> //
> //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X 
> ${matrix} \//
> //--C ${C1} \//
> //--glmdir ${odir} --surf fsaverage ${h} ${surf}//
> //
> //*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir}
> --cache ${t} pos*//*
> */
> Note: it is the same code i use for the t-tests, which appear to
> work fine.
>
> The content of the file ${C1} is
>
> 1   -1  0   0   0   0
> 1   0  -1   0   0   0
>
>
> Thanks in advance!
>
> Nicola
>
>
>
> On 7/21/2016 5:38 PM, Douglas N Greve wrote:
>> what is your mri_glmfit-sim command line?
>>
>> On 07/20/2016 05:56 PM, Nicola Toschi wrote:
>>> Hi List,
>>>
>>> I am getting a couple of strange error when running a 3-group
>>> F-test.
>>>
>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>> WARNING: 251446 NaNs found in volume
>>> analysis/Ftest/cache.th20.pos.sig.cluster.mgh...
>>>
>>> And as a result, I consistently get huge clusters:
>>>
>>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX MNIY MNIZ CWP
>>> CWPLowCWPHi   NVtxsWghtVtx   Annot
>>>1  inf   0  63247.45 -38.8 -19.0 66.9 
>>> 0.00010
>>> 0.0  0.00020  98722 inf precentral
>>>
>>> However, this doesn't happen when running t-tests on the 
>>> same data.
>>> Still, I think my F-contrast is correct (see below).
>>>
>>> Thanks in advance for any advice!
>>>
>>> Nicola
>>>
>>> PS:
>>>
>>> my F-contrast looks like this:
>>>
>>> 1   -1  0   0 

[Freesurfer] Freesurfer 6.0?

[Trisanna Sprung-Much]

Hi there

Do we have a potential date for the Freesurfer 6.0 release? I was told I
would want to re-run all my subjects to create better surfaces using
Freesurfer 6.0 and I am wondering if it really will improve surface
extraction that much.

Many thanks!

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
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Re: [Freesurfer] question about reslicing

[Bruce Fischl]

Hi Dorsa

did you create the aseg.mgz from 1mm data (using the standard "conform" 
process), or higher res? The file you sent is higher:


mri_info resliceduncoregtahalmus.nii.gz
Volume information for resliceduncoregtahalmus.nii.gz
  type: nii
dimensions: 512 x 512 x 288
   voxel sizes: 0.488281, 0.488281, 0.625000
  type: SHORT (4)
   fov: 250.000
   dof: 0
xstart: -125.0, xend: 125.0
ystart: -125.0, yend: 125.0
zstart: -90.0, zend: 90.0
TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees

   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present


it also has strange values in it (-32K and 32K, so probably things that 
can't be represented as a short). Does your aseg.mgz look right?


cheers
Bruce


On 
Mon, 25 Jul 2016, 
Dorsa Haji Ghaffari wrote:



Hi, This is the command line for reslicing:
mri_convert -rl aseg.mgz thalamus.nii resliceduncoregtahalmus.nii

thalamus.nii is the thalamus mask obtained by using the following command:
mri_binarize --i aseg.mgz --match 10 --o thalamus.mask.nii.gz

and I have attached the out put.

Thank you!

On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl 
wrote:
  Hi Dorsa

  you need to give us more details. What was your reslicing
  command line? And the screen output?

  Bruce
  On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:


Hi,

I re-sliced my left thalamus so that the size and
number of slices correspond with the original MRI,
but when I open it in freeview, it shows an extra
part(
like a cube) on the bottom of the image ( I have
attached the  mask). do you have any idea how to
solve that? 
Also how can I make sure that the position and size
of the thalamus makes sense since the thalamus mask
has a different slice size and number than the
original mri?

Thank you

Dorsa



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Re: [Freesurfer] : cortical thickness ceiling (using an ROI mask)

[Bruce Fischl]

Hi Kari

what do you mean when you say "when I look at them in freeviewer the voxels 
are definitely not in the correct spot". Do you mean the spectroscopy 
voxels?

cheers
Bruce



On Fri, 22 Jul 2016, Kari Parsons wrote:

> Hi Bruce,
>
> Yes, I agree it doesn't seem right.  They're LAG and ACG (I'm using 
> spectroscopy voxels as my ROIs).  The surfaces look reasonable when I'm 
> running through the suggested steps on the freesurfer website for getting 
> the surface thickness when using an roi as a mask, but when I look at 
> them in freeviewer the voxels are definitely not in the correct spot 
> (they're pretty far off).
>
> The acquisition parameters for the scan were pretty standard (BRAVO 
> sequence with 1 mm^3 isotropic voxels).  The steps that I ran through 
> with the spectroscopy voxel were:
>
> tkmedit -f ${subj_T1} -overlay ${spectroscopy_voxel_mask} -fthresh 0.5
>
> mri_vol2surf --mov ${spectroscopy_voxel_mask} --hemi lh --out 
> lh.${subj_number}.ACG.mgh
>
> cd ${subj_number}/surf
>
> tksurfer ${subj_number} lh inflated -overlay lh.${subj_number}.ACG.mgh 
> -fthresh 0.5
>
> mri_surf2surf --s ${subj_number} --trgsubject ${subj_number} --hemi lh --sval 
> lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
>
> mri_segstats --seg lh.${subj_number}.ACG.mgh --in 
> ${subj_number}/surf/lh.thickness.fsaverage.mgh --sum 
> segstats-${subj_number}.txt
>
> Thanks very much,
> Kari
>
> On 2016-06-02, at 6:53 PM, Bruce Fischl  wrote:
>
>> Hi Kari
>>
>> the average thickness in some ROIs is 5mm??? Like which ones? That
>> certainly seems like something is wrong. Do the surfaces look accurate?
>> What were the parameters/resolution/sequence of the data you gave to
>> recon-all?
>>
>> cheers
>> Bruce
>>
>>
>>  On Fri, 3 Jun 2016, Kari Parsons wrote:
>>
>>> Hi,
>>>
>>>I'm using ROI masks (spectroscopy voxels) to get cortical thickness 
>>> values.  I'm pretty much following the tutorial online 
>>> ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer.  It looks 
>>> like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and 
>>> I'm getting that as the maximum cortical thickness for a fair number of 
>>> subject's ROI.  I'd really like to hear thoughts on this: if it might be 
>>> indicative of some error happening and if my mean or range cortical 
>>> thickness is going to be thrown off by it?
>>>
>>> Thanks for your help,
>>> Kari
>>>
>>>
>>>
>>> ___
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>>>
>>>
>>>
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>> properly
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>>
>
>
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>
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Re: [Freesurfer] question about reslicing

[Bruce Fischl]

Hi Dorsa

you need to give us more details. What was your reslicing command line? 
And the screen output?


Bruce
On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:



Hi,

I re-sliced my left thalamus so that the size and number of slices correspond 
with the original MRI, but when I open it in freeview, it shows an extra part(
like a cube) on the bottom of the image ( I have attached the  mask). do you 
have any idea how to solve that? 
Also how can I make sure that the position and size of the thalamus makes sense 
since the thalamus mask has a different slice size and number than the
original mri?

Thank you

Dorsa


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Re: [Freesurfer] bbregister problem in FS5.1

[Fred Sampedro]

Hi Douglas,

Thank you very much for answering. Unfortunately, I can read all the files
without any problem in FSL/SPM, and I still have more than 40GB of free
space. In fact, running the exact same instruction in freesurfer 5.3 works
fine.

:(



On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve 
wrote:

> It looks like one of two things:
>
> 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM,
> AFNI) can read the file
>
> 2. You have run out of disk space
>
> On 7/24/16 10:52 AM, Fred Sampedro wrote:
>
> Dear FS experts,
>
> I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm
> trying to run bbregister to register a AV45-PET image to its corresponding
> FS processed T1 image. For that, I'm trying to run:
>
> bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
>
> And I keep getting segfaults:
>
> Log file is register.dat.log
> dom jul 24 16:44:19 CEST 2016
>
> $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
> Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14
> UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> FREESURFER_HOME /usr/local/freesurfer
> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
> ./tmp.bbregister.5353/template.nii
> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz
> ./tmp.bbregister.5353/template.nii
> Segmentation fault (core dumped)
>
>
> I have tried the same installation and command in two different computers
> and obtained the same segfault. I have also tried the same pipeline using
> instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz
> and get the same result. I didn't have this issue using freesurfer 5.3, but
> I need to use 5.1 for an ongoing project.
>
> I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2
> Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
>
> Any help would be much appreciated,
>
> Thanks a lot in advance,
>
> Fred Sampedro
>
>
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Re: [Freesurfer] Checking segmentations with aseg.mgz

[Reema Jayakar]

Hi Dr. Fischl,

Thank you for clarifying that about norm.mgz for checking segmentations.
Good to know that brain and brainmask wash out low contrast borders.

Cheers,
Reema


-- 
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu

On Mon, Jul 18, 2016 at 4:42 PM, Reema Jayakar 
wrote:

> Hello FS Listserv members,
>
> With regard to checking amygdala segmentation, is it appropriate to
> overlay the aseg.mgz file on the brainmask.mgz? Or should I be overlaying
> aseg.mgz on norm.mgz? I am aware of the general rule of thumb that
> editing the subcortical segmentations generally is not recommended.
>
> Also, where can I find documentation on the Freeview options "Resample to
> standard RAS space" and
>
> "Apply registration file". I am trying to understand whether or not it is 
> necessary for me to use any of these options for what I am doing with the 
> subcortical segmentations.
>
>
> Thanks in advance for your help!
>
> Reema
>
>
>
> --
> *Reema Jayakar, M.A.*
> Doctoral Candidate - Clinical Neuropsychology
> Health Resources and Services Administration (HRSA) Fellow
> Department of Psychology
> Georgia State University
> Email: rjayak...@student.gsu.edu
>
>
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Re: [Freesurfer] normalizing in fsgd

[Douglas Greve]

No, that flag does not exist, but it is a good idea! You'll have to 
normalize them by hand.



On 7/24/16 1:33 PM, miracle ozzoude wrote:

Hello freesurfer experts,
I am trying to normalize my continuous variables in my fsgd file. Is 
this the correct term to add to my fsgd file in order for mri_glmfit 
to normalize it?


GroupDescriptorFile 1
Title PCS
Class group1
Class group2
Normalize 1
Variables Age Education Scoreone Scoretwo
Input 053 group1 47 18 3.4 5.6
Input 054 group2 50 16 5.3 2.8

Thank you,
Paul


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Re: [Freesurfer] bbregister problem in FS5.1

[Douglas Greve]

It looks like one of two things:

1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, 
AFNI) can read the file


2. You have run out of disk space


On 7/24/16 10:52 AM, Fred Sampedro wrote:

Dear FS experts,

I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and 
I'm trying to run bbregister to register a AV45-PET image to its 
corresponding FS processed T1 image. For that, I'm trying to run:


bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1

And I keep getting segfaults:

Log file is register.dat.log
dom jul 24 16:44:19 CEST 2016

$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 
17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

FREESURFER_HOME /usr/local/freesurfer
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz 
./tmp.bbregister.5353/template.nii
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz 
./tmp.bbregister.5353/template.nii

Segmentation fault (core dumped)


I have tried the same installation and command in two different 
computers and obtained the same segfault. I have also tried the same 
pipeline using instead the FS version 
freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same 
result. I didn't have this issue using freesurfer 5.3, but I need to 
use 5.1 for an ongoing project.


I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 
2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.


Any help would be much appreciated,

Thanks a lot in advance,

Fred Sampedro


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Re: [Freesurfer] mri_label2label volume registration problem

[Douglas Greve]

When you use --regmethod volume, it assumes that the label coordinates 
are in native anatomical space and then applies the mni305 registration 
(talairach.xfm). In this case, your source subject is fsaverage so the 
native space is assumed to be mni305 space (and talairach.xfm is the 
identity). So if you don't start with mni305, the the output surely 
won't be right. Second, when you use --regmethod volume, any surface 
information will be lost (or inappropriate), which is probably why you 
are seeing such chaos on the surface. I think by far the best solution 
is to use --regmethod surface. Talairach is so inaccurate that 0-4mm of 
misalignment is meaningless.



On 7/25/16 9:23 AM, Agoston Mihalik wrote:


Hi Freesurfer Developers,

I would like to ask for your expertise in the following problem I 
encountered:


I want to create subject specific labels based on a label I created in 
fsaverage. The transformation needs to be based on Talairach 
intermediate registration, since my label was drawn based on Talairach 
coordinates.


I ran the following command:

mri_label2label --srclabel test.label --srcsubject fsaverage 
--trglabel lh.test2.label --trgsubject


subj222 --regmethod volume

The problem is that the output label is scattered and all around the 
place when I look at it in tksurfer - see the image attached 
(lh.regmethod_volume.tif).


When I did the registration based on surface, it worked fine (see the 
image also attached - lh.regmethod_volume.tif), however, it resulted 
in 0-4 mm misalignment when I looked at the Talairach coordinates of 
the label borders. I guess it is due to the surface registration that 
optimises the surfaces to be aligned, not the Talairach coordinates.


Please find some information attached in case it is any help – content 
of files, output etc.


Here is my freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0

Your help would be really appreciated.

Thanks and best,

Agoston



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Re: [Freesurfer] How to apply ACPC alignment to Freesurfer output

[Douglas Greve]

If you have a registration matrix that maps to the desired orientation, 
then you can apply it to a segmentation with mri_label2vol. But why not 
just register the anatomical to the DTI (bbregister) and then run 
mri_label2vol with that registration to map the WM mask directly into 
the native DTI space?



On 7/25/16 7:56 AM, Sandra Hanekamp wrote:

Dear Freesurfer community,

I would like to apply ACPC alignment to Freesurfer output.

Data was previously segmented with recon -all and a lot of manual 
editing using ITK. Unfortunately, the data was not aligned to ACPC and 
this causes errors in my pipeline (I am using the labels and white 
matter mask from Freesurfer for my DTI analysis).


Re-doing the segmentation plus necessary edits would be very 
time-consuming due to a poor contrast between white and grey matter 
and the number of scans that I have, so I would prefer to align the 
current output to ACPC. Does anyone know a solution that does not 
involve re-doing the segmentation? How can I apply ACPC alignment to 
Freesurfer output?


Thank you so much for any thoughts or recommendations you might be 
able to provide.


Sandra Hanekamp
Laboratory for Experimental Ophthalmology
University Medical Center Groningen



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Re: [Freesurfer] ERROR: cannot find volume matching

[Douglas Greve]

What is the exact name of the file that you are trying to include as a 
taskreg?



On 7/25/16 12:26 AM, Erik Jahner wrote:

Dear Free Surfer experts

I am attempting to run a functional connectivity analysis on some 
resting state data. However, I keep getting stuck in this final step 
of the online Functional Connectivity Pathway. I have made a change 
based on discussion boards, but it do not help. CHANGE: in the 
mkanalysis step, I changed the "-taskreg L_Posteriorcingulate.dat 1" 
to "-taskreg L_Posteriorcingulate 1”. This did not solve the problem. 
My mkanalysis lines are as follows:


mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh 
-fwhm 5 -notask -taskreg L_Posteriorcingulate 1 -nuisreg vcsf.dat 5 
-nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR TR2 -hpf 
.01 -force -per-run


mkanalysis-sess -analysis fc.lpccseed.surf.rh -surface fsaverage rh 
-fwhm 5 -notask -taskreg L_Posteriorcingulate 1 -nuisreg vcsf.dat 5 
-nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR TR2 -hpf 
.01 -force -per-run


mkanalysis-sess -analysis fc.lpccseed.surf.mni305 -mni305 -fwhm 5 
-notask -taskreg L_Posteriorcingulate 1 -nuisreg vcsf.dat 5 -nuisreg 
wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR TR2 -hpf .01 
-force -per-run


I then run the following:

selxavg3-sess -s 401 -a fc.lpccseed.surf.lh -overwrite

and the error that is produced is as follows: (what does "cannot find 
volume …” mean? and how might I fix this)


/Applications/freesurfer/LagStructure/413
-
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
/Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/Applications/freesurfer/matlab/MRIread.m
-
outtop = /Applications/freesurfer/LagStructure
Extension format = nii.gz
ERROR: cannot find volume matching 
/Applications/freesurfer/LagStructure/413/rest/001/L_Posteriorcingulate
ERROR: loading nonpar reg 
/Applications/freesurfer/LagStructure/413/rest/001/L_Posteriorcingulate

--
ERROR: fast_selxavg3() failed\n


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[Freesurfer] flipping TRACULA tracts

[Barbara Kreilkamp]

Dear Freesurfers,

I've got data pertaining to patients with left and right-sided temporal 
lobe epilepsy (TLE).
My aim is to group those tracts according to side of epilepsy for 
waypoint comparisons.

Basically for patients with right TLE I'd like to look at right tracts 
and at the same time for patients with left TLE I'd like to look at left 
tracts (ipsilateral tracts), I need to do the same for the contralateral 
tracts.
Is there a straightforward way of doing this?

I've already copied the tracts to respective ipsi and contralateral 
byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt; 
do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in 
R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i 
${i/byvoxel./byvoxel_contraRTLE.}; done
Now I have to flip the x-coordinates in the patients with right TLE (to 
make them more comparable to the tracts of the patients with left TLE). 
That will not be a problem, but I wonder if I am missing something?
Can I then just go ahead and run trac-all -stats -c dmrircfile to 
generate the mean waypoint tracts etc.?

Thank you very much,
Best wishes,

Barbara

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[Freesurfer] LME for surface area

[Clara Kühn]

Dear FreeSurfer Experts,

I'm following the LME tutorial to analyze my data. The example that is given in 
the tutorial is for a left hemispheric cortical thickness analysis. I would 
also like to look at surface area. Would I follow the same steps? At the point 
in the tutorial that uses the lme_mass_fit_Rgw command I have to specify a 
Distance type (euc or surf). How would I do that regarding surface area? Would 
I have to skip this step or is there a similar command or does it just work 
with different arguments? Unfortunately, surface area isn't mentioned in LME 
tutorial.

Thanks for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] mri_label2label volume registration problem

[Agoston Mihalik]

Hi Freesurfer Developers,

I would like to ask for your expertise in the following problem I encountered:

I want to create subject specific labels based on a label I created in 
fsaverage. The transformation needs to be based on Talairach intermediate 
registration, since my label was drawn based on Talairach coordinates.

I ran the following command:
mri_label2label --srclabel test.label --srcsubject fsaverage --trglabel 
lh.test2.label --trgsubject
subj222 --regmethod volume

The problem is that the output label is scattered and all around the place when 
I look at it in tksurfer - see the image attached (lh.regmethod_volume.tif).

When I did the registration based on surface, it worked fine (see the image 
also attached - lh.regmethod_volume.tif), however, it resulted in 0-4 mm 
misalignment when I looked at the Talairach coordinates of the label borders. I 
guess it is due to the surface registration that optimises the surfaces to be 
aligned, not the Talairach coordinates.

Please find some information attached in case it is any help - content of 
files, output etc.

Here is my freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0

Your help would be really appreciated.

Thanks and best,
Agoston



info.rtf
Description: info.rtf
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[Freesurfer] How to apply ACPC alignment to Freesurfer output

[Sandra Hanekamp]

Dear Freesurfer community,

I would like to apply ACPC alignment to Freesurfer output. 

Data was previously segmented with recon -all and a lot of manual editing using 
ITK. Unfortunately, the data was not aligned to ACPC and this causes errors in 
my pipeline (I am using the labels and white matter mask from Freesurfer for my 
DTI analysis). 

Re-doing the segmentation plus necessary edits would be very time-consuming due 
to a poor contrast between white and grey matter and the number of scans that I 
have, so I would prefer to align the current output to ACPC. Does anyone know a 
solution that does not involve re-doing the segmentation? How can I apply ACPC 
alignment to Freesurfer output?

Thank you so much for any thoughts or recommendations you might be able to 
provide. 

Sandra Hanekamp
Laboratory for Experimental Ophthalmology
University Medical Center Groningen

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[Freesurfer] Post Doc Position advert!

[Muthuraman Muthuraman]

*Post-Doc*





*Neuroscientist with focus on multimodal brain imaging*





The *medical faculty of the University of Mainz*, Germany, invites

applications for a



Post Doc Position





for a functional translational neuroscience (FTN) scholarship two years
position to work on multi-modal imaging, neurostimulation (TMS) and EEG.
 Additionally, the new position requires experience with structural and
functional MRI data analysis, computational modeling or magnetic diffusion
imaging. The candidate should have a PhD or equivalent degree preferably in
neuroscience, biomedical physics, psychology, psychiatry, or biology and
should be able to supervise experiments and data analyses in programming
platforms. The working language at the institute is English.



The location for this research will mainly be the workgroups “Section of
movement disorders, neurostimulation and neuroimaging” of Prof. Sergiu
Groppa at the Department of Neurology and “Biomedical statistics and
multimodal signal processing unit” of Prof. Muthuraman Muthuraman, both at
the Focus Program Translational Neurosciences (http://www.ftn.uni-mainz.de/)
and Neuroimaging Centre Mainz (http://www.ftn.nic.uni-mainz.de/) and within
the CRC “Neurobiology of resilience to stress-related mental dysfunction”
and SFB TR-128 “Initiating/effector versus regulatory mechanisms in
Multiple Sclerosis”  (www.sfbtr128.de). Expected close collaborations with
national and international partners.







The application should include a statement of research interests and
reasons for applying to the project, curriculum vitae (max. 4 pages)
composed according to good scientific practice.



The position will be open until filled. To apply for the position, please
send the above documents to *Prof.* *Sergiu Groppa and Prof. Muthuraman
Muthuraman*, Department of Neurology, Section of Movement Disorders and
Neurostimulation, University of Mainz, Langenbeckstrasse 1, 55131
Mainz, Germany, or by Email to *segroppa(at)uni-mainz.de
 & mmuthura(at)uni-mainz.de *.
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[Freesurfer] TRACULA fornix tractography

[Barbara Kreilkamp]

Dear Anastasia,

As we are analyzing DTI data acquired in patients with epilepsy we are 
especially interested in the fornix.
I've come across the mri_cc -f option for fornix segmentation (native 
space) but I've also read that manual tracing/labeling of the tracts 
would be needed in the 33 controls for TRACULA (training set - trctrain).
In Wakana et al. 2011 I see that the fornix was not included due to low 
reproducibility and it further states:


"the reason for the poor reproducibility is most likely due to not 
enough spatial resolution with respect to the diameter"


I wonder if you could please guide us in how to best add this tract to 
TRACULA so that it would be consistent in the methods compared with the 
other tract ROI definitions or perhaps state what were the difficulties 
in adding this particular tract to TRACULA.


Thank you very much,
Best wishes,
Barbara
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