Re: [Freesurfer] gnumeric file

[Bruce Fischl]

Hi Caroline

the data are in native space. Summary statistics means e.g. the volume of 
the left hippocampus. You don't need any registration algorithm for this 
type of thing - you just tabulate it across subjects


cheers
Bruce


On Thu, 17 Mar 2016, Caroline Beelen wrote:


Hi Bruce,

Thank you very much! :)
I think somethings wrong with gnumeric indeed just discovered that gedit 
works fine.

As for 3, that would mean that the data are not in native space? I'm trying to understand 
this concept of "summary statistics" :-).

Thanks again in advance.

Caroline



-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 13:59
Aan: Freesurfer support list 
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
something strange with gnumeric and I'm not sure we are qualified to help you.

As for 3, the tables contain summary stats and so don't need to be mapped into 
any common space.

cheers
Bruce


On Thu, 17 Mar 2016, Caroline
Beelen wrote:



Dear FS,

 

1. I typed: aparcstats2table --hemi lh --meas thickness --subjects
A01_T1


A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed
by)

gnumeric lh.aparc.thickness.table. As soon as I typed in the latter,
it generated the table attached. Why are the mean cortical thickness
values sometimes depicted wrong and how can I change this (or do I
need to do this by hand)?

 

2. I noticed aparcstats2table doesn’t generate a mean volume (column
AJ is empty). Is that supposed to be the case?

 

3. A final question: the aparcstats2table and asegstats2table contain
data in native space. Before loading Qdec data needs to be smoothed
onto the average subject (using qcache). As s I understand correctly
from your answer below and the tutorial I could either just use these
values to create the qdectable.dat file or just load the tables in Qdec itself.

Does that mean that the values of these tables somehow (have)
change(d) during the smoothing process?

 

Sorry if my questions are rather basic…, but I try to fully
understand. J

Thanks again for responding in advance.

 

Kind regards,

 

Caroline


 


 

 

Van: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file

 

 

On 3/16/16 6:52 AM, Caroline Beelen wrote:

  Hi FS team,

   

  Sorry for these rather basic questions…

   

  I'm not sure whether the gnumeric file is an ascii file (see
  mails below). Attached you'll find the file. It seems the case
  when you open it in the terminal screen that the nr's look fine
  (with command cat). However as soon as you type the command
  gnumeric and so on, it creates a wrong table from the start (see
  file attached). Can I somehow change this?

How did you create this file? The aparcstats2table command produces a
simple ascii file.

   

  I have an additional question:

  I was looking at the Qdec info (tutorial) and I am not totally
  sure how to create the table.dat file… Where to get the volume
  measures from, if you’d like to include those? The statistical
  folder (where the tables are from)?

Run asegstats2table and/or aparcstats2table to create a table of the
volumes, then extract the values you need. BTW, you don't have to have
volume measures in the qdec table.

   

  Thank you for responding in advance.

   

  Kind regards, Caroline

   

  -Oorspronkelijk bericht-

  Van: freesurfer-boun...@nmr.mgh.harvard.edu
  [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
  Greve

  Verzonden: dinsdag 8 maart 2016 0:24

  Aan: freesurfer@nmr.mgh.harvard.edu

  Onderwerp: Re: [Freesurfer] mean thickness

   

  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!

 >

 > 

Re: [Freesurfer] WM edit, remove GM bright rim

[Bruce Fischl]

Hi Min

unfortunately there's not much we can do as these artifacts make the gray 
matter look just like white matter. Do you see this in many subjects?



sorry
Bruce


On Thu, 17 Mar 2016, Min Liu wrote:


Dear Bruce, 
Many thanks for looking into this. I tried to post orig.mgz to the mailing
list yesterday but the email didn't get through because the file size
exceeds 1000KB.  So I screen-captured two images to showcase the overall
quality of T1 and where the problem is.  Although the bright rim doesn't
occur everywhere, it is mostly seen in the left hemisphere.  I hope there is
a way to counteract such acquisition defects.

Thanks,
Min

On Wed, Mar 16, 2016 at 6:51 PM, Bruce Fischl 
wrote:
  Hi Min

  that looks like it might be a normalization problem. Can you
  post the orig.mgz and see what it looks like? Is there a bright
  rim in it also?

  cheers
  Bruce
  On Wed, 16 Mar 2016, Min Liu wrote:

Dear Freesufer users,
We have some T1 images having a rim of bright signal
in the GM at some spots
like the one showing in the attached Figure 1.  The
WM surface goes out to
include this bright signal and the cortex ends up
artificially thin.  We
followed the standard WM edit procedure, which is to
erase the bright signal
in wm.mgz. As shown in Figure 2, the bright rim is
replaced with intensity 1
(red). However, that doesn't improve the situation. 
Does anyone know a way
to prevent the surface from going out?

Thanks,


--
Min


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Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

Hi Elisabeth

we don't have an exact date yet, but have finished our code modifications 
(hopefully!) and are in the process of freezing a version after which we 
will run a set of tests and hopefully release it

cheers
Bruce


On Wed, 16 Mar 
2016, Elisabeth Paul wrote:

> Dear ladies and gentlemen,
> 
> for a research project I need to measure the volume of the different
> hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can only
> find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if so,
> when will it be released? If it is already released, could you tell me where
> to find it?
> 
> Thank you very much in advance.
> 
> Kind regards,
> 
> Elisabeth Paul
> 
>
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Re: [Freesurfer] error - mri_nu_correct.mni

[Flavia Niccolini new]

Hi Douglas,

I have done this but I got the following error:

[hwilson@nig05 ~]$ cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
[hwilson@nig05 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
--no-rescale --i orig.mgz --o orig_nu.mgz
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
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
Wed 16 Mar 10:09:44 GMT 2016
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.13997
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13997/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13997/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.13997/nu0.mnc...
 

Iteration 1 Wed 16 Mar 10:09:47 GMT 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.13997/nu0.mnc 
./tmp.mri_nu_correct.mni.13997/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.13997/0/ -iterations 1000 -distance 50
nu_correct: Command not found.
ERROR: nu_correct
[hwilson@nig05 mri]$ 


any suggestions?

Many Thanks

With Best Wishes

Flavia




> On 15 Mar 2016, at 16:30, Douglas N Greve  wrote:
> 
> It should all be on one line
> 
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
> --i orig.mgz --o orig_nu.mgz
> 
> 
> 
> On 03/14/2016 05:43 AM, Flavia Niccolini new wrote:
>> Hi Douglas,
>> 
>> I have done this and I got the following message:
>> 
>> “cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>> hwilson@nig05 mri]$   mri_nu_correct.mni --n 1 --proto-iters 1000 
>> --distance 50 --no-rescale
>> ERROR: must specify an input volume
>> hwilson@nig05 mri]$ --i orig.mgz --o orig_nu.mgz “
>> 
>> 
>> Many Thanks
>> 
>> With Best Wishes
>> 
>> Flavia
>> 
>> 
>> 
>> 
>>> On 7 Mar 2016, at 23:51, Douglas N Greve >> > wrote:
>>> 
>>> 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 

[Freesurfer] GM mask to native T1

[Patrick Beukema]

I am attempting to align the GM mask (lh.ribbon.mgz) to the T1 in native
space. I see this thread that states this command is the correct way:

mri_label2vol --seg lh.ribbon.mgz --temp rawavg.mgz --o
ribbon-in-rawavg.mgz --regheader ribbon.mgz

from:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33578.html

However, when I do do, the alignment is off. All of my rawavg.mgz are
rotated relative to the original T1 in native space, so the GM masks are
also not properly aligned. Is there a transformation that I am missing
somewhere between rawavg.mgz and native T1?

Thank you,
Patrick
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Re: [Freesurfer] Replacing / turning off denoising filter

[Mojmír Vinkler]

Thanks!

Just FYI - we applied newer version of NLME from Pierrick Coupé before
running freesurfer and it greatly improved segmentation results.

On Wed, Mar 16, 2016 at 3:47 PM Bruce Fischl 
wrote:

> Hi Mojmir
>
> we don't apply mri_nlfilter by default so there is no need to turn it
> off. You are welcome to try it out. It implement some nonlinear filters
> including what is now called nonlocal means as described in this paper:
>
>
> http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?reload=true=745732
>
>
> cheers
> Bruce
>
> On
> Wed, 16 Mar 2016, Mojmír Vinkler wrote:
>
> > Hi,
> > I was wondering if it's possible to replace or turn off your denoising
> > algorithm `mri_nlfilter`. We'd like to try different denoising filters
> and
> > compare how they influence segmentation performance. Right now we're
> > applying filter before running recon-all, but I fear that applying your
> > filter on already filtered image might degrade our analysis.
> >
> > I couldn't find any mention of mri_nlfilter besides this one on mailing
> listhttps://
> mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020762.
> > html. I hope I didn't miss something anything.
> >
> > Thanks!
> > Mojmir
> >
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[Freesurfer] HIRING: Research Assistant

[Rockers, Elijah D.]

Hello,

The Houston Methodist Research Institute is hiring for a research 
assistant position. Please see the attached document for details. Please 
also note that candidates must be able to work in the city of Houston 
day-to-day.

If you are interested in applying, please follow the instructions enclosed.

Thank you,

Elijah

Houston Methodist. Leading Medicine.

Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 
specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" 
list 10 years in a row. Designated as a Magnet hospital for excellence in 
nursing. Visit us at houstonmethodist.org. Follow us at 
twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 
Hospital and/or its relevant affiliates and may contain restricted and 
privileged material for the sole use of the intended recipient(s). Any review, 
use, distribution or disclosure by others is strictly prohibited. If you are 
not the intended recipient (or authorized to receive for the recipient), please 
contact the sender and delete all copies of the message. Thank you.


ResearchAssistantPsychology.docx
Description: ResearchAssistantPsychology.docx
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Re: [Freesurfer] mris_flatten error: bad vertex

[Ji Won Bang]

Dear. Bruce.

Thanks a lot for your help!

I attached the tar.gz file for mri below.

If you need anything more, let me know.

Thanks,
Ji Won​
 replay06_mri.tar.gz

​

2016-03-17 11:40 GMT-04:00 Bruce Fischl :

> Hi Ji
>
> that does sound strange! Can you tar and gzip the subject and upload it to
> our website so I can see if I can replicate the problem?
>
> cheers
> Bruce
>
>
> On Thu, 17 Mar 2016, Ji Won Bang wrote:
>
> > Dear. Freesurfer experts.
> >
> > Hi.
> >
> > I'm having a problem with mris_flatten (version 5.3.0)
> >
> >
> > Could you please help me fix this problem?
> >
> > My command line is:
> > mris_flatten -w 0 -distances 12 7
> $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
> > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
> >
> > It returns the error:
> > using write iterations = 0
> > sampling 7 neighbors out to a distance of 12 mm
> > reading patch
> /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d
> > with 30434 vertices (20.5% of total)
> > MRISreadPatch: bad vertex # (148517) found in patch file
> > No such file or directory
> >
> > When making the patch lh.oc.patch.3d, I followed the processes below:
> > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
> > -contrast UpperLower
> >
> > select 3 points along a boundary between upper and lower visual fields
> (near
> > calcarine sulcus) and press "Cut line". Then, select 4 points to define
> the
> > cutting plane: 1 on lower side of the line, 2 on upper side of the line,
> 3
> > on the opposite surface (use rotation tool), and 4 to specify which
> portion
> > of surface is kept, and press "Cur plane". File->Patch->Save Patch As
> > lh.oc.patch.3d
> >
> > So I think I made the patch correctly.
> >
> > ! weird thing that I suspect is that when I click save patch as, the
> default
> > location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to
> > $SUBJECTS_DIR/$SUBJECT/surf
> >
> > Could you please help me?
> >
> > Thanks a lot!
> >
> > Best,
> > Ji Won
> >
> >
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[Freesurfer] Anterior to Posterior Length

[Heather Acuff]

Good morning,

I apologize if this email was sent out twice.  I would like to use anterior to
posterior length as a covariate in my DTI analysis.  Is there an easy way
to obtain this information for each subject?

Thank you,
Heather
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[Freesurfer] ID not identified on surface file

[João V. Dornas]

Dear Friends,

I need to 3D render the AAL parcellation volume, with labels (in annotation 
file) for each ROI.

My AAL volume is on MNI152 standard space, with 2mm 91x109x91, as well my 
results volumes.

I used the following command to generate my surface files from my AAL volume.

mri_vol2surf --mov aal2std.nii.gz --reg 
cvs_avg35_inMNI152/mri/transforms/reg.mni152.2mm.dat --projdist-max 0 1 0.1 
--interp nearest --hemi lh --out lh.aal2std-1mm_surf.mgz —reshape

mri_vol2surf --mov aal2std.nii.gz --reg 
cvs_avg35_inMNI152/mri/transforms/reg.mni152.2mm.dat --projdist-max 0 1 0.1 
--interp nearest --hemi rh --out rh.aal2std-1mm_surf.mgz --reshape

Then I tried to create my labels using the following command:

mri_cor2label --i lh.aal2std-1mm_surf.mgz --surf cvs_avg35_inMNI152 lh --id 75 
--l lh.Pallidum_L

I run this command for each one of the 90 ROIs on AAL volume.

My problem is that when I execute the last command specifically for Pallidum, 
both Left and Right (IDs 75 and 76), I found this error:

$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
Loading mri lh.aal2std-1mm_surf.mgz
Loading cvs_avg35_inMNI152/surf/lh.white
Scanning the volume
Found 0 label voxels
ERROR: found no voxels matching id 75  


It seems that I loose some voxels when I convert from volume voxels to surface 
vertexes.

Do you know what could be happening?

I appreciate any help you could give to us.

Thanks very much,

best regards,

--  
João V. Dornas
Phd student in Neuroscience
Cognitive Biology Group, Institute of Biology
Otto von Guericke University, Magdeburg
Germany

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Re: [Freesurfer] aparc stats volume outputting area instead

[Clare Loane]

Hi Doug,

Many thanks indeed: everything working fine now.

BW

clare

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 16 March 2016 14:53
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparc stats volume outputting area instead


There is not actually a "-meas" option. It should be either " -m volume" or " 
--measure=volume". Strange, it should have exited with an error but some reason 
it did not and used area as the default.

On 3/16/16 10:27 AM, Clare Loane wrote:

Hi Doug,

I am using version 5.3 and the terminal output does not state an error (below) 
and the file is created (attached) but as you will see, it is the area 
measurements which are output.

dcnmac75:Freesurfer clare$ aparcstats2table --subjects CON_001 CON_002 CON_003 
CON_004 CON_006 CON_007 CON_008 CON_009 CON_010 CON_011 CON_013 CON_014 CON_015 
CON_016 CON_017 CON_018 CON_019 CON_021 CON_022 CON_025 CON_026 CON_027 CON_028 
CON_029 CON_030 CON_032 CON_033 CON_034 CON_035 CON_036 CON_038 CON_039 CON_040 
CON_041 CON_042 CON_045 CON_049 CON_054 CON_055 CON_057 CON_063 OXCON_005 
OXCON_009 OXCON_012 OXCON_025 OXCON_026 OXCON_028 OXCON_029 OXCON_031 OXCON_040 
OXCON_042 OXCON_052 OXCON_053 OXCON_054 OXCON_055 OXCON_058 OXCON_059 OXCON_060 
OXCON_061 OXCON_062 OXCON_064 OXCON_065 OXCON_066 OXCON_067  --hemi rh –meas 
volume --tablefile aparc_stats_volume_rh.txt --skip
SUBJECTS_DIR : /Users/clare/Desktop/MAP/Volumetrics/FreeSurfer/CONTROLS/
Parsing the .stats files
Building the table..
Writing the table to aparc_stats_volume_rh.txt

Since posting the original message, it does seem that the correct measurement 
can be acquired when I aparcstat2table on subjects individually. Although often 
it will state error that the rh.aparc.stats is not found or is too small to be 
a valid stats file. This is not the case as they are all there and full of 
measurements.

Many thanks,

Clare



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 15 March 2016 16:55
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparc stats volume outputting area instead

Can you send the terminal output? Also, what version are you using?

On 03/14/2016 09:56 AM, Clare Loane wrote:


Hi,

I am trying to pull out the volumes from the aparc stats file but when
I input the following (below) it produces a file identical to the area
instead:

aparcstats2table --subjects 001 002 003 --hemi rh --meas volume
--tablefile aparc_stats_volume_rh.txt

It works fine for thickness and area as well aseg_stats.

I would appreciate any help with this.

Thank you!

Clare


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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Hippocampal subfield segmentation with T1

[Eugenio Iglesias]

Hi Xiaowei,
this was my mistake when I wrote the article in the wiki. The images do not 
need to be in the same orientation (I already changed this in the wiki). They 
need to be coarsely registered in physical coordinates (i.e., the need to look 
approximately registered when you open them in FreeView). If you manually 
rotate / translate the T2, make sure that you check the "do not resample" box 
when you save the rotated scan in order not to lose information.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Bruce Fischl" 
To: "Xiaowei Zhuang" 
Cc: "Freesurfer support list" 
Sent: Wednesday, March 16, 2016 11:16:48 PM
Subject: Re: [Freesurfer] Hippocampal subfield segmentation with T1

Hi Xiaowei

you can try mri_robust_register --cost nmi or --cost mi, then give the 
resulting transform to mri_convert -at transform.lta -rl T2.mgz


The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will 
have the same geometry. You can also try mri_coreg if you like instead of 
mri_robust_register if it doesn't work well

cheers
Bruce


On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote:

> 
> Dear Freesurfer expert,
> 
>  
> 
> I am using Freesurfer V6.0 beta version to run the hippocampal subfield
> segmentation with 2 inputs, a standard T1 and a high resolution T2.
> 
>  
> 
> Below are the details about the 2 images.
> 
>  
> 
> T1: resolution: 0.8*0.8*0.8 mm,  orientation: Sagittal(S>T4.1>C-0.8)
> 
> T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5).
> 
>  
> 
> The instruction says in order to use both of them for hippocampal
> segmentation, T2 should be in the same orientation as T1. Therefore, the two
> images cannot be used directly.
> 
>  
> 
> Is it possible for me to do some reorient preprocess on the T2 image and
> then run through the segmentation?
> 
>  
> 
> Or is it possible to coregister the T1 into T2 space, making them both high
> resolution and run through the segmentation? Will this affect the Freesurfer
> pipeline and the final subfields output?
> 
>  
> 
> Any suggestion will help.
> 
>  
> 
> Sincerely thanks,
> 
> Xiaowei.  
> 
>  
> 
>  
> 
>  
> 
> Cleveland Clinic logo
> 
>  
> 
> Xiaowei Zhuang   |  Research Engineer  |  Lou Ruvo Center for Brain
> Health
> 
>  Cleveland Clinic  |  888 W Bonneville Ave.   |  Las Vegas, NV
> 89106  | (702) 685-6051
> 
>  
> 
>  
> 
> ===
> 
> Please consider the environment before printing this e-mail
> 
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[Freesurfer] Regarding: running lgi with freesurfer dev6 and matlab2016a

[Dr Sampada Sinha]

Dear freesurfer expert Marie,

I am trying to run lgi after doing recon-all. I am getting stuck with an
error. Just wanted to know if freesurfer dev6 is compatible with newest
Malta 2016a version.

Thanks and regards,

Sampada
Predoctoral student
KGMU, Lucknow
India


-- 
Sampada Sinha
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Re: [Freesurfer] Anterior to Posterior Length

[Bruce Fischl]

Hi Heather

the anterior/posterior length of each tract you mean? Or the length of 
the entire hemi?

Bruce
On Wed, 16 Mar 2016, Heather Acuff wrote:


Good morning,

I apologize if this email was sent out twice.  I would like to
use anterior to posterior length as a covariate in my DTI analysis.  Is
there an easy way to obtain this information for each subject?

Thank you,
Heather

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Re: [Freesurfer] Smoothing at FWHM (Qdec)

[Bruce Fischl]

Hi Martin

there is no easy answer to this question. Basically, the optimal 
smoothing filter depends on the size of the effect you are looking for 
(the so-called "matched-filter theorem"). IN general, if you have bigger 
groups of subjects and/or expect focal differences use a smaller kernel.

Sorry I don't have better advice to give than that
cheers
Bruce

On Wed, 16 Mar 2016, Martin Juneja 
wrote:

> Hello everyone,
> I am very new to FreeSurfer. Although I know what smoothing means etc. but I
> am not sure what smoothing level is the best to choose while comparing
> cortical thinning for patients vs. controls. Qdec gives several options to
> choose from among 0, 5, 10, 15, 20 and 25.
> Literature says 10 mm is the typical value to choose but when I calculate
> clusters, I don't see any significant clusters (at FDR p < 0.05) but at
> smoothing level 20 mm, I can see several clusters at the same threshold i.e.
> at FDR p < 0.05.
> 
> I would really appreciate if someone, expert in this field could guide me
> regarding this. Also, may be if someone could recommend me a few papers from
> literature discussing this issue e.g. effect of smoothing on cortical
> thickness etc., that would be very useful.
> 
> Thanks,
> MJ
> 
>
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Re: [Freesurfer] error while running dt-recon all

[Jasmin Alves]

Do you mean, what ends up happening? I have attached a screen shot of what
files are made.



On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve 
wrote:

> Can you send me what dt_recon prints to the screen when your run the
> command below?
>
>
> On 3/15/16 11:40 PM, Jasmin Alves wrote:
>
> Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o
> /Users/jasminalves/Desktop/data/FREESURFER/40
>
> INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/
>
> dt_recon logfile
>
> Tue Mar 15 20:37:35 PDT 2016
>
> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
>
> setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/
>
> cd /Users/jasminalves/Desktop/data/40
>
> /Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
> /Users/jasminalves/Desktop/data/FREESURFER/40
>
> Jasmins-MacBook-Pro.local
>
> jasminalves
>
> /Applications/Utilities/fsl/bin/eddy_correct
>
> ECRefTP 0
>
> #@#---
>
> Converting input
>
> Tue Mar 15 20:37:35 PDT 2016
>
> cd /Users/jasminalves/Desktop/data/40
>
> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>
> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...
>
> TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-0.29, 0.0116015, -0.00282784)
>
> j_ras = (0.0115984, 0.32, 0.00109136)
>
> k_ras = (-0.00284031, -0.00105848, 0.95)
>
> writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...
>
> cd /Users/jasminalves/Desktop/data/40
>
> mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>
> Jasmins-MacBook-Pro:40 jasminalves$
>
>
>
> On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Can you send the full terminal output from when you run dt_recon with
>> the nifti as input?
>>
>> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
>> > How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
>> > dicom data using dcm2nii.
>> >
>> > Response for: "What happens if you run mri_info DTI.nii.gz"
>> >
>> > Volume information for DTI.nii.gz
>> >
>> >   type: nii
>> >
>> > dimensions: 128 x 128 x 70 x 65
>> >
>> >voxel sizes: 2., 2., 2.
>> >
>> >   type: FLOAT (3)
>> >
>> >fov: 256.000
>> >
>> >dof: 0
>> >
>> > xstart: -128.0, xend: 128.0
>> >
>> > ystart: -128.0, yend: 128.0
>> >
>> > zstart: -70.0, zend: 70.0
>> >
>> > TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>> > angle: 0.00 degrees
>> >
>> >nframes: 65
>> >
>> >PhEncDir: UNKNOWN
>> >
>> > ras xform present
>> >
>> > xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =
>> >   -0.4290
>> >
>> >   : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a =
>> > 4.1548
>> >
>> >   : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =
>> >   30.9622
>> >
>> > Orientation   : LAS
>> >
>> > Primary Slice Direction: axial
>> >
>> > voxel to ras transform:
>> >
>> >-1.   0.0232 -0.0057   126.2761
>> >
>> > 0.0232   1. -0.0021  -125.2474
>> >
>> >-0.0057   0.0022 2.   -38.8153
>> >
>> > 0.   0. 0. 1.
>> >
>> > voxel-to-ras determinant -8
>> >
>> > ras to voxel transform:
>> >
>> >-0.5000   0.0058 -0.001463.8052
>> >
>> > 0.0058   0.5000 0.000561.9083
>> >
>> >-0.0014  -0.0005 0.500019.5206
>> >
>> > 0.   0. 0. 1.
>> >
>> >
>> > On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve
>> > > wrote:
>> >
>> >
>> > How was DTI.nii.gz created? What happens if you run
>> > mri_info DTI.nii.gz
>> >
>> > If the DICOM is a siemens dicom but has been stripped of special
>> > siemens
>> > info, then we cannot unpack it
>> >
>> >
>> > On 03/15/2016 02:02 PM, Jasmin Alves wrote:
>> > >
>> > > Still get the same error:
>> > >
>> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
>> > > contain a Siemens ASCII header
>> > >
>> > > has this file been anonymized?
>> > >
>> > > ERROR: cannot unpack mosiacs without ASCII header
>> > >
>> > >
>> > > The error I get when running in nifti format is actually found
>> > in the
>> > > log file.
>> > >
>> > >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a
>> dicom
>> > > file or some other problem
>> > >
>> > >
>> > >
>> > >
>> > > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
>> > > 

[Freesurfer] preproc-sess in longitudinal stream

[Ji Won Bang]

Dear. Freesurfer experts.

Hi. How are you?

I have dataset where a single subject was scanned twice on different days.

I ran recon-all in logitudinal stream (cross, base, long).
The recon-all -base gave me the within-subject template and the recon-all
-long gave me the directory in the format of tp1id.long.templateID.
By doing so, I get different time point's norm.mgz (under
tp1id.long.templateID directory and tp2id.long.templateID etc) aligned in
the same voxel space.

As a next step, I'd like to register the functional scans to the anatomical
scans via preproc-sess (or mc-sess, spmregister-sess etc).
I guess, the anatomical can that I should use is norm.mgz under
tp1id.long.templateID directory and tp2id.long.templateID etc. (?)

To register the functional scans to the newly created anatomical image
obtained from recon-all -long process (norm.mgz under tp1id.long.templateID
directory and tp2id.long.templateID etc), I think I should specify this
newly created norm.mgz in the command line... but couldn't figure it out
yet.

The preproc-sess command that I used in the cross-sectional process is as
below:
preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_decode -per-run -force
-fwhm 0

What should I do to make registration process target a specific anatomical
image?

Please give me any advice!

Thank you so much for your help!

Best,
Ji Won
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Re: [Freesurfer] aparc stats volume outputting area instead

[Douglas Greve]

There is not actually a "-meas" option. It should be either " -m volume" 
or " --measure=volume". Strange, it should have exited with an error but 
some reason it did not and used area as the default.


On 3/16/16 10:27 AM, Clare Loane wrote:

Hi Doug,

I am using version 5.3 and the terminal output does not state an error (below) 
and the file is created (attached) but as you will see, it is the area 
measurements which are output.

dcnmac75:Freesurfer clare$ aparcstats2table --subjects CON_001 CON_002 CON_003 
CON_004 CON_006 CON_007 CON_008 CON_009 CON_010 CON_011 CON_013 CON_014 CON_015 
CON_016 CON_017 CON_018 CON_019 CON_021 CON_022 CON_025 CON_026 CON_027 CON_028 
CON_029 CON_030 CON_032 CON_033 CON_034 CON_035 CON_036 CON_038 CON_039 CON_040 
CON_041 CON_042 CON_045 CON_049 CON_054 CON_055 CON_057 CON_063 OXCON_005 
OXCON_009 OXCON_012 OXCON_025 OXCON_026 OXCON_028 OXCON_029 OXCON_031 OXCON_040 
OXCON_042 OXCON_052 OXCON_053 OXCON_054 OXCON_055 OXCON_058 OXCON_059 OXCON_060 
OXCON_061 OXCON_062 OXCON_064 OXCON_065 OXCON_066 OXCON_067  --hemi rh –meas 
volume --tablefile aparc_stats_volume_rh.txt --skip
SUBJECTS_DIR : /Users/clare/Desktop/MAP/Volumetrics/FreeSurfer/CONTROLS/
Parsing the .stats files
Building the table..
Writing the table to aparc_stats_volume_rh.txt

Since posting the original message, it does seem that the correct measurement 
can be acquired when I aparcstat2table on subjects individually. Although often 
it will state error that the rh.aparc.stats is not found or is too small to be 
a valid stats file. This is not the case as they are all there and full of 
measurements.

Many thanks,

Clare



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 15 March 2016 16:55
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparc stats volume outputting area instead

Can you send the terminal output? Also, what version are you using?

On 03/14/2016 09:56 AM, Clare Loane wrote:

Hi,

I am trying to pull out the volumes from the aparc stats file but when
I input the following (below) it produces a file identical to the area
instead:

aparcstats2table --subjects 001 002 003 --hemi rh --meas volume
--tablefile aparc_stats_volume_rh.txt

It works fine for thickness and area as well aseg_stats.

I would appreciate any help with this.

Thank you!

Clare


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[Freesurfer] mri_glmfit-sim ( cluster wise analysis)

[Alshikho, Mohamad J.]

Dear FS experts,
I ran cortical thickness analysis as previously explained in Wiki :

Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis


1.   My data is previously cached so I ran the command : mris_preproc 
--fsgd gender_age.fsgd  --cache-in thickness.fwhm10.fsaverage  --target 
fsaverage --hemi lh  --out lh.gender_age.thickness.10.mgh

2.   GLM analysis: mri_glmfit  --y lh.gender_age.thickness.10.mgh  --fsgd 
gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx  --surf fsaverage lh  
--cortex  --glmdir lh.gender_age.glmdir

3.   Correction for multiple comparison  mri_glmfit-sim  --glmdir 
lh.gender_age.glmdir  --cache 4 neg  --cwp  0.05  --2spaces

In order to do cluster-wise correction for multiple comparisons, I ran the 
command "mri_glmfit-sim" (step3). This command is calling, internally, the 
command "mri_surfcluster" as follow:

mdline mri_surfcluster --in lh//2G0C/sig.mgh --csd 
/usr/local/freesurfer/stable5_3_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd
 --mask lh//mask.mgh --cwsig lh//2G0C/cache.th13.pos.sig.cluster.mgh --vwsig 
lh//2G0C/cache.th13.pos.sig.voxel.mgh --sum 
lh//2G0C/cache.th13.pos.sig.cluster.summary --ocn 
lh//2G0C/cache.th13.pos.sig.ocn.mgh --oannot 
lh//2G0C/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf 
lh//2G0C/cache.th13.pos.pdf.dat --cwpvalthresh 0.05 --o 
lh//2G0C/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white


Kindly, I have the following questions:


1.   How the command mri_surfcluster choose the fwhm for the flag "csd" . 
In the previous command it shows fwhm=15.

2.   What is purpose of using the flag Bonferroni in the previous command

3.   If we are doing cluster wise correction, what is theexact usage of the 
flag "--vwsig"


Thanks for your patience !
Looking forward to learn from you


Mohamad
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[Freesurfer] Reg: Correcting Defect error

[Jesu Kiran Jk]

Dear Freesurfer experts,

I have been running freesurfer for a patient data, and have to find this
retesselalation of defect. I have successful with some data but for some
others it looks frozen even after 7 days. Would it be possible to please
have a look and help me out? Also, how could I pass on the data?

Looking forward for your kind reply,

Kind regards,
Jesu
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Re: [Freesurfer] Replacing / turning off denoising filter

[Bruce Fischl]

Hi Mojmir

we don't apply mri_nlfilter by default so there is no need to turn it 
off. You are welcome to try it out. It implement some nonlinear filters 
including what is now called nonlocal means as described in this paper:


http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?reload=true=745732


cheers
Bruce

On 
Wed, 16 Mar 2016, Mojmír Vinkler wrote:



Hi,
I was wondering if it's possible to replace or turn off your denoising
algorithm `mri_nlfilter`. We'd like to try different denoising filters and
compare how they influence segmentation performance. Right now we're
applying filter before running recon-all, but I fear that applying your
filter on already filtered image might degrade our analysis.

I couldn't find any mention of mri_nlfilter besides this one on mailing 
listhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020762.
html. I hope I didn't miss something anything.

Thanks!
Mojmir

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Re: [Freesurfer] error while running dt-recon all

[Douglas Greve]

Can you send me what dt_recon prints to the screen when your run the 
command below?


On 3/15/16 11:40 PM, Jasmin Alves wrote:


Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o 
/Users/jasminalves/Desktop/data/FREESURFER/40


INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/

dt_recon logfile

Tue Mar 15 20:37:35 PDT 2016

VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $

setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/

cd /Users/jasminalves/Desktop/data/40

/Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o 
/Users/jasminalves/Desktop/data/FREESURFER/40


Jasmins-MacBook-Pro.local

jasminalves

/Applications/Utilities/fsl/bin/eddy_correct

ECRefTP 0

#@#---

Converting input

Tue Mar 15 20:37:35 PDT 2016

cd /Users/jasminalves/Desktop/data/40

mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz 
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii


mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz 
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii


$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...

TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.29, 0.0116015, -0.00282784)

j_ras = (0.0115984, 0.32, 0.00109136)

k_ras = (-0.00284031, -0.00105848, 0.95)

writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...

cd /Users/jasminalves/Desktop/data/40

mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz

Jasmins-MacBook-Pro:40 jasminalves$



On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve 
> wrote:


Can you send the full terminal output from when you run dt_recon with
the nifti as input?

On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
> dicom data using dcm2nii.
>
> Response for: "What happens if you run mri_info DTI.nii.gz"
>
> Volume information for DTI.nii.gz
>
>   type: nii
>
> dimensions: 128 x 128 x 70 x 65
>
>voxel sizes: 2., 2., 2.
>
>   type: FLOAT (3)
>
>fov: 256.000
>
>dof: 0
>
> xstart: -128.0, xend: 128.0
>
> ystart: -128.0, yend: 128.0
>
> zstart: -70.0, zend: 70.0
>
> TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> angle: 0.00 degrees
>
>nframes: 65
>
>PhEncDir: UNKNOWN
>
> ras xform present
>
> xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028,
c_r =
>   -0.4290
>
>   : x_a =   0.0116, y_a =   0., z_a =  -0.0011,
c_a =
> 4.1548
>
>   : x_s =  -0.0028, y_s =   0.0011, z_s =   1.,
c_s =
>   30.9622
>
> Orientation   : LAS
>
> Primary Slice Direction: axial
>
> voxel to ras transform:
>
>-1.   0.0232 -0.0057   126.2761
>
> 0.0232   1. -0.0021  -125.2474
>
>-0.0057   0.0022 2.   -38.8153
>
> 0.   0. 0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>
>-0.5000   0.0058 -0.001463.8052
>
> 0.0058   0.5000 0.000561.9083
>
>-0.0014  -0.0005 0.500019.5206
>
> 0.   0. 0. 1.
>
>
> On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve
> 
>> wrote:
>
>
> How was DTI.nii.gz created? What happens if you run
> mri_info DTI.nii.gz
>
> If the DICOM is a siemens dicom but has been stripped of special
> siemens
> info, then we cannot unpack it
>
>
> On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> >
> > Still get the same error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001
does not
> > contain a Siemens ASCII header
> >
> > has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > The error I get when running in nifti format is actually found
> in the
> > log file.
> >
> >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is
not a dicom
> > file or some other problem
> >
> >
> >
> >
> > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > 

Re: [Freesurfer] tksurfer

[Douglas Greve]

it looks like the cluster is covering most of the brain, including 
precentral gyrus. The precentral gyrus ROI in the table file indicates 
that is where the peak of the cluster is and does not mean that the 
cluster is confined to that ROI


On 3/16/16 9:43 AM, John Anderson wrote:

Dear experts,
I am running into a trouble visualizing my data in tksurfer. I highly 
appreciate any advice that can help!
I ran group analysis between two groups using GLM analysis 
(mri_glmfit) and I corrected the results for multiple comparison using 
(mri_glmfit-sim), then I ran this command to visualize the results:

tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh
The result attached. In my summary file I see that I have significant 
differnce only in the precentral gyrus. But the results in tksurger is 
not showing precentral gyrus. I tried to play with the thresholds and 
nothing changed.

Any advice is highly appreciated!!
Bests,
John


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Re: [Freesurfer] FWHM file not found

[pedrogomesrosa]

Many thanks!

> On Mar 16, 2016, at 15:18, Marie Schaer  wrote:
> 
> 
> You still have to “smooth” even if you choose fwhm=0 to project the data in 
> the fsaverage space. 
> 
> So if I were you I would start with fwhm=5mm, check in the qdec console what 
> is the final fwhm of your data (or check the fwhm.dat in the glmdir folder), 
> and if you thinks it’s too high (I’d say >20mm), then go for fwhm=0mm, which 
> should solve the problem.
> 
> But the ideal if 5mm is too high is to smooth still a bit, by 1 or 2mm, if 
> you are ok to go without qdec.
> 
> 
> 
>> On 16 Mar 2016, at 11:13, Pedro Rosa  wrote:
>> 
>> Thanks for que quick answer, Marie.
>> If I got right, I should either not smooth it after mri_preproc (no 
>> mri_surf2surf) or do it with kernels < 5mm, and that should make to FMHM 
>> fall below 30. Am I correct?
>> Thanks,
>> Pedro.
>> 
>>> On Wed, Mar 16, 2016 at 3:03 PM, Marie Schaer  wrote:
>>> 
>>> Hi Pedro,
>>> 
>>> So lGI is inherently very smoothed, and you don’t want to over smooth 
>>> (which is why you get this error), so I usually recommend either no 
>>> smoothing (fwhm=0) or fwhm=5mm, given that these are the options easily 
>>> inputed in qdec. I’d say try first with 5mm, and check if this work, if it 
>>> doesn't decrease to 0mm. And if you want then to work around, you can tune 
>>> your smoothing with values in between to achieve a smoothness level of 
>>> 15mm, most often with 1 or 2mm, but qdec won’t accept it so you’ll have to 
>>> go for the commandline stats.
>>> 
>>> Hope it helps,
>>> 
>>> Marie
>>> 
>>> 
>>> 
>>> 
>>> 
>>> > On 16 Mar 2016, at 10:50, Pedro Rosa  wrote:
>>> >
>>> > Dear FreeSurfers,
>>> > I am running a localgi analysis using mri_glmfit and mri_glmfit-sim, and 
>>> > it seems the last script looked for 
>>> > freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/fwhm40/abs/th13/mc-z.cdf
>>> >  and mc-z.csd, but there are precached data until fmhm30.
>>> > How should I proceed?
>>> > Best,
>>> > Pedro.
>>> > ___
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>>> >
>>> >
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>>> > is
>>> > addressed. If you believe this e-mail was sent to you in error and the 
>>> > e-mail
>>> > contains patient information, please contact the Partners Compliance 
>>> > HelpLine at
>>> > 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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>> properly
>> dispose of the e-mail.
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Re: [Freesurfer] Problems with file un qdec analysis

[Lisa Delalande]

that's what I thought !
Thanks a lot for your help !

Best regards !
Lisa

2016-03-15 17:31 GMT+01:00 Douglas N Greve :

> you cannot have more than two levels of a factor in qdec. You can use
> the "command line" stream. See the wiki
>
> On 03/14/2016 06:52 AM, Lisa Delalande wrote:
> > Hello everyone,
> >
> > I've got some problems with qdec. I have .levels with more than 2
> > factors. For example a "grpe.levels" with three factors : children
> > (enfant), adults (adultes) and nothing (rien). But if I want to
> > exclude some subjects like children qdec doesn't work anymore
> > (attachment : error message). Is that possible a .levels can not have
> > more than two factors ? Or the problem came from anything else ?
> >
> > Thanks in advance for your help !
> > Best regards,
> >
> > Lisa
> >
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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>
>
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> is
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] FWHM file not found

[Pedro Rosa]

Thanks for que quick answer, Marie.
If I got right, I should either not smooth it after mri_preproc (no
mri_surf2surf) or do it with kernels < 5mm, and that should make to FMHM
fall below 30. Am I correct?
Thanks,
Pedro.

On Wed, Mar 16, 2016 at 3:03 PM, Marie Schaer  wrote:

>
> Hi Pedro,
>
> So lGI is inherently very smoothed, and you don’t want to over smooth
> (which is why you get this error), so I usually recommend either no
> smoothing (fwhm=0) or fwhm=5mm, given that these are the options easily
> inputed in qdec. I’d say try first with 5mm, and check if this work, if it
> doesn't decrease to 0mm. And if you want then to work around, you can tune
> your smoothing with values in between to achieve a smoothness level of
> 15mm, most often with 1 or 2mm, but qdec won’t accept it so you’ll have to
> go for the commandline stats.
>
> Hope it helps,
>
> Marie
>
>
>
>
>
> > On 16 Mar 2016, at 10:50, Pedro Rosa  wrote:
> >
> > Dear FreeSurfers,
> > I am running a localgi analysis using mri_glmfit and mri_glmfit-sim, and
> it seems the last script looked for
> freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/fwhm40/abs/th13/mc-z.cdf
> and mc-z.csd, but there are precached data until fmhm30.
> > How should I proceed?
> > Best,
> > Pedro.
> > ___
> > 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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Re: [Freesurfer] tksurfer

[John Anderson]

Thank you doug,

Please what do you suggesst me to do?

Is this related to something wrong in the analysis?
 

Bests,
John

 

Sent: Wednesday, March 16, 2016 at 10:42 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tksurfer





it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI
 
On 3/16/16 9:43 AM, John Anderson wrote:



Dear experts,

I am running into a trouble visualizing my data in tksurfer. I highly appreciate any advice that can help!

I ran group analysis between two groups using GLM analysis (mri_glmfit) and I corrected the results for multiple comparison using (mri_glmfit-sim), then I ran this command to visualize the results:

 

tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh 

 

The result attached. In my summary file I see that I have significant differnce only in the precentral gyrus. But the results in tksurger is not showing precentral gyrus. I tried to play with the thresholds and nothing changed.

 

Any advice is highly appreciated!!

Bests,
John 

 

 
 

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Re: [Freesurfer] AAL 3D rendering with subcorticals

[Douglas Greve]

Did you check the volume to verify that at least one voxel has an index 
= 75 ?


On 3/19/16 10:43 AM, João V. Dornas wrote:

Dear friends,

I am following this procedures to plot a 3D rendering of the AAL 
volume 
(https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html).


My problem is the following. When I execute this command:

*mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L*

*
*

specifically for the ROI Pallidum, a subcortical ROI, I receive the 
following error



/$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $/

/Loading mri lh.Colin27_aal2std.mgh/

/Loading 
/Applications/freesurfer/subjects/FS_spm_CanonicalBrain/surf/lh.white/


/Scanning the volume/

/Found 0 label voxels/

/ERROR: found no voxels matching id 75 /


This happens both for Pallidum Left and Pallidum Right, but all other 
AAL ROI work fine. I have an almost complete 3D rendering for my AAL. 
Only these subcortical regions are missing.


Someone knows what could be happening?

Thanks for the help.

best,

--
João V. Dornas
Phd student in Neuroscience
Cognitive Biology Group, Institute of Biology
Otto von Guericke University, Magdeburg
Germany



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Re: [Freesurfer] cannot allocate memory

[Douglas Greve]

that's going to create a pretty big volume as it will map your 
functional time course to a 256^3 float volume. If you have 100 time 
points, then that will be about 7G.


On 3/16/16 3:27 PM, Ehsan Tadayon wrote:

Hi Bruce,

Thanks for your response. I'm using :

freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 
on OS X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command 
that I'm using:


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


Thanks in advance for your help.

best regards,
Ehsan.




On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl 
> wrote:


Hi Ehsan

We need the full command line and screen output and also what your
hardware and software environments are to help you. Certainly
sounds like you ran out of memory though

Cheers
Bruce

> On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon
> wrote:
>
> Ehsan

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Re: [Freesurfer] Replacing / turning off denoising filter

[Bruce Fischl]

that's interesting. Is it open source? If so, can you point us at it? Maybe 
someone should compare it to the version I wrote 20 years ago :)


On Fri, 18 Mar 2016, Mojmír Vinkler wrote:


Thanks!
Just FYI - we applied newer version of NLME from Pierrick Coupé before
running freesurfer and it greatly improved segmentation results.

On Wed, Mar 16, 2016 at 3:47 PM Bruce Fischl 
wrote:
  Hi Mojmir

  we don't apply mri_nlfilter by default so there is no need to
  turn it
  off. You are welcome to try it out. It implement some nonlinear
  filters
  including what is now called nonlocal means as described in this
  paper:

http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?reload=true=745
  732


  cheers
  Bruce

  On
  Wed, 16 Mar 2016, Mojmír Vinkler wrote:

  > Hi,
  > I was wondering if it's possible to replace or turn off your
  denoising
  > algorithm `mri_nlfilter`. We'd like to try different denoising
  filters and
  > compare how they influence segmentation performance. Right now
  we're
  > applying filter before running recon-all, but I fear that
  applying your
  > filter on already filtered image might degrade our analysis.
  >
  > I couldn't find any mention of mri_nlfilter besides this one
  on 
mailinglisthttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020
  762.
  > html. I hope I didn't miss something anything.
  >
  > Thanks!
  > Mojmir
  >
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Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

[Joseph Dien]

I did more digging around and came up with a procedure.  Please let me know if 
it would cause any problems.
Looking at the contents of the X.mat files (which contain the predictors), it 
appears that the betas are indeed arranged as c1 d1 c2 d2…
I also found that isxconcat-sess requires the contrast output of 
mkcontrast-sess so I can’t just bypass it.

So my thought is:

1) run mkanalysis-sess with -spmhrf 1
2) run selxavg3-sess with the -no-con-ok flag to get the spmhrf1 betas without 
bothering with the contrasts
3) run mkanalysis-sess with -spmhrf 0
4) run selxavg3-sess again but with the contrasts to get everything set up
5) read in the spmhrf1 betas with MRIread and compute the Calhoun derivative 
boost with the beta values in mri.vol
6) use these values to compute the desired contrasts.  From my examination of a 
sample ces.nii.gz file, a simple linear combination based on the contrast 
weights is all that is needed.
7) replace the contents of the corresponding spmhrf0 ces.nii.gz files’ mri.vol 
with these new values
8) write out the new ces.nii.gz files.
9) proceed with the analysis stream, using isxconcat-sess to set up the second 
level analysis

So the question is, would this work?  Am I neglecting files other than 
ces.nii.gz that would need to be modified?  or other fields in the mri data 
structure?
When you referred to writing “out a new volume” is this what you meant?

Thanks again for this help!

Joe


> On Mar 15, 2016, at 17:32, Joseph Dien  wrote:
> 
> oh duh!  Sorry, wasn’t thinking clearly.
> Okay, I see how to generate the betas now.  I don’t even need to mess with 
> the mkcontrast-sess command.
> I just run selxavg3-sess with the -no-con-ok flag.
> With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex.
> With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex.
> With 12 conditions, 12 more betas is exactly right.
> So how do I know which of the betas is which?
> I looked through the files and couldn’t find any labels.
> I’m guessing the first twelve are the condition betas for "spmhrf 0".
> If so, for "spmhrf 1", is it arranged as:
> 
> 1) c1 c2 c3…d1 d2 d3...
> 
> or
> 
> 2) c1 d1 c2 d2...
> 
>  (where d is the first derivative term)
> 
> also, when I asked you earlier about implementing this procedure, I had 
> suggested reading the betas, computing the Calhoun, then generating new 
> beta.nii.gz files with the new betas replacing the original spmhrf0 betas and 
> then continuing with the regular analysis stream but you said it would result 
> in invalid p-values.  Instead, you suggested:
> 
> "I was just thinking you could load the beta into matlab, make the
> Calhoun computations on each condition, then compute the contrasts, then
> write out the new volume”
> 
> can you expand on how one might “compute the contrasts” and “write out the 
> new volume”?
> 
> Thanks again for this help!
> 
> Joe
> 
> 
>> On Mar 15, 2016, at 12:43, Douglas N Greve > > wrote:
>> 
>> The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
>> 
>> On 03/13/2016 10:29 PM, Joseph Dien wrote:
>>> After a long break, back to this…
>>> 
>>> My goal is still to get the betas for the first and maybe second spm 
>>> hrf so I can calculate a Calhoun derivative boost measure.
>>> 
>>> As a first step I ran:
>>> 
>>> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh 
>>> -fwhm 5 -event-related  -paradigm RPA1fix.par -nconditions 12 -spmhrf 
>>> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg 
>>> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
>>> 
>>> to use the SPM HRF with one derivative.
>>> 
>>> Then:
>>> 
>>> selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
>>> 
>>> I got the following error:
>>> 
>>> ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch
>>> This condition has 2 regressors, but evrm has 1
>>> Struct contents reference from a non-struct array object.
>>> 
>>> Error in flac_conmat (line 37)
>>> if(nthcon > length(flac.con))
>>> 
>>> Error in flac_customize (line 369)
>>>  flacnew = flac_conmat(flacnew,nthcon);
>>> 
>>> Error in fast_selxavg3 (line 65)
>>> flac0 = flac_customize(flac0);
>>> 
> --
>>> ERROR: fast_selxavg3() failed\n
>>> 
>>> This ran fine with spmhrf 0
>>> 
>>> based on your prior response below that:
>>> 
>>> "This is what happens. If you want to use the derivatives,
>>> then you need to spec -setwdelay. When you run the command, it will 
>>> prompt you
>>> for 3 values to use. If you spec 1 0 0, then it will be the same as the
>>> default. If you want to test only the first derivative, then 
>>> you would spec 0 1 0. Note that the 3rd regressor is the 2nd 
>>> derivative wrt time, not the first derivative wrt the dispersion 
>>> parameter. You
>>> cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
>>> 
>>> I tried:
>>> 
>>> 

[Freesurfer] AAL 3D rendering with subcorticals

[João V. Dornas]

Dear friends,  

I am following this procedures to plot a 3D rendering of the AAL volume 
(https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html).

My problem is the following. When I execute this command:

mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L

specifically for the ROI Pallidum, a subcortical ROI, I receive the following 
error

$Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $
Loading mri lh.Colin27_aal2std.mgh
Loading /Applications/freesurfer/subjects/FS_spm_CanonicalBrain/surf/lh.white
Scanning the volume
Found 0 label voxels
ERROR: found no voxels matching id 75  

This happens both for Pallidum Left and Pallidum Right, but all other AAL ROI 
work fine. I have an almost complete 3D rendering for my AAL. Only these 
subcortical regions are missing.

Someone knows what could be happening?

Thanks for the help.

best,

--  
João V. Dornas
Phd student in Neuroscience
Cognitive Biology Group, Institute of Biology
Otto von Guericke University, Magdeburg
Germany

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Re: [Freesurfer] gnumeric file

[Douglas Greve]

On 3/16/16 6:52 AM, Caroline Beelen wrote:


Hi FS team,

Sorry for these rather basic questions…

I'm not sure whether the gnumeric file is an ascii file (see mails 
below). Attached you'll find the file. It seems the case when you open 
it in the terminal screen that the nr's look fine (with command cat). 
However as soon as you type the command gnumeric and so on, it creates 
a wrong table from the start (see file attached). Can I somehow change 
this?


How did you create this file? The aparcstats2table command produces a 
simple ascii file.


I have an additional question:

I was looking at the Qdec info (tutorial) and I am not totally sure 
how to create the table.dat file… Where to get the volume measures 
from, if you’d like to include those? The statistical folder (where 
the tables are from)?


Run asegstats2table and/or aparcstats2table to create a table of the 
volumes, then extract the values you need. BTW, you don't have to have 
volume measures in the qdec table.


Thank you for responding in advance.

Kind regards, Caroline

-Oorspronkelijk bericht-

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 
Namens Douglas N Greve


Verzonden: dinsdag 8 maart 2016 0:24

Aan: freesurfer@nmr.mgh.harvard.edu 



Onderwerp: Re: [Freesurfer] mean thickness

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



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Re: [Freesurfer] FreeSurfer 6.0

[Martin Reuter]

Although it should be mentioned that outputs (even of subfields) are 
going to change due to differences in the regular freesurfer processing, 
as the subfields stream builds upon the regular FS stream.

Best, Martin


On 03/16/2016 10:52 AM, Eugenio Iglesias wrote:
> I only changed some details (e.g., temporary directories) that do not affect 
> the output.
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> - Original Message -
> From: "Bruce Fischl" 
> To: "Freesurfer support list" 
> Sent: Wednesday, March 16, 2016 3:49:31 PM
> Subject: Re: [Freesurfer] FreeSurfer 6.0
>
> yes, although the hippocampal stuff hasn't changed I don't think
> (Eugenio: is that correct)?
>
> On Wed, 16 Mar 2016, Alan Francis wrote:
>
>> Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
>> ran the HSF method successfully. Have they retracted that version?
>>
>> best,
>>
>> Alan
>>
>> On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl 
>> wrote:
>>actually there is no beta yet, but hopefully within a week or so
>>On Wed, 16 Mar 2016, Alan Francis wrote:
>>
>>  Hi Elizabeth:
>>
>>  I ran the Hippocampal subfields on 6.0 beta. The
>>  parcellation looks great.
>>  Beta is available for download. Here is the URL:
>>
>>  https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>
>>  best,
>>
>>  Alan
>>
>>  On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
>>   wrote:
>>Dear ladies and gentlemen,
>>
>>  for a research project I need to measure the volume
>>  of the different
>>  hippocampus subregions. I want to use FreeSurfer 6.0
>>  for that but I
>>  can only find FreeSurfer 5.3 online. Is FreeSurfer
>>  6.0 not yet
>>  released and if so, when will it be released? If it
>>  is already
>>  released, could you tell me where to find it?
>>
>>  Thank you very much in advance.
>>
>>  Kind regards,
>>
>>  Elisabeth Paul
>>
>>  ___
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>>
>>
>>  The information in this e-mail is intended only for
>>  the person to whom
>>  it is
>>  addressed. If you believe this e-mail was sent to
>>  you in error and the
>>  e-mail
>>  contains patient information, please contact the
>>  Partners Compliance
>>  HelpLine at
>>  http://www.partners.org/complianceline . If the
>>  e-mail was sent to you
>>  in error
>>  but does not contain patient information, please
>>  contact the sender
>>  and properly
>>  dispose of the e-mail.
>>
>>
>>
>>
>>  --
>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>  Alan N. Francis PhD
>>  NIDA T32  Fellow in Computational Neuroscience
>>  Brain Imaging Center
>>  McLean Hospital
>>  Harvard Medical School
>>  115 Mill Street, Belmont, MA 02478
>>  al...@bwh.harvard.edu
>>  afran...@mclean.harvard.edu
>>  
>> 
>>   
>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>
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>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> --
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> Alan N. Francis PhD
>> NIDA T32  Fellow in Computational Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>   

Re: [Freesurfer] FreeSurfer 6.0

[Eugenio Iglesias]

I only changed some details (e.g., temporary directories) that do not affect 
the output.


Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Bruce Fischl" 
To: "Freesurfer support list" 
Sent: Wednesday, March 16, 2016 3:49:31 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0

yes, although the hippocampal stuff hasn't changed I don't think 
(Eugenio: is that correct)?

On Wed, 16 Mar 2016, Alan Francis wrote:

> Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
> ran the HSF method successfully. Have they retracted that version?
> 
> best,
> 
> Alan
> 
> On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl 
> wrote:
>   actually there is no beta yet, but hopefully within a week or so
>   On Wed, 16 Mar 2016, Alan Francis wrote:
>
> Hi Elizabeth:
>
> I ran the Hippocampal subfields on 6.0 beta. The
> parcellation looks great.
> Beta is available for download. Here is the URL:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> best,
>
> Alan
>
> On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
>  wrote:
>       Dear ladies and gentlemen,
>
> for a research project I need to measure the volume
> of the different
> hippocampus subregions. I want to use FreeSurfer 6.0
> for that but I
> can only find FreeSurfer 5.3 online. Is FreeSurfer
> 6.0 not yet
> released and if so, when will it be released? If it
> is already
> released, could you tell me where to find it?
>
> Thank you very much in advance.
>
> Kind regards,
>
> Elisabeth Paul
>
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> Alan N. Francis PhD
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Re: [Freesurfer] Regarding: running lgi with freesurfer dev6 and matlab2016a

[Dr Sampada Sinha]

Sorry for the typos...its Matlab 2016a version I meant!

On Wednesday, March 16, 2016, Dr Sampada Sinha 
wrote:

> Dear freesurfer expert Marie,
>
> I am trying to run lgi after doing recon-all. I am getting stuck with an
> error. Just wanted to know if freesurfer dev6 is compatible with newest
> Malta 2016a version.
>
> Thanks and regards,
>
> Sampada
> Predoctoral student
> KGMU, Lucknow
> India
>
>
> --
> Sampada Sinha
>
>
>
>
>
>
>
>
>
>
>

-- 
Sampada Sinha
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[Freesurfer] Per-vertex regression model

[Sophie Maingault]

Hello FS experts,
I would like to correlate for each vertex 2 anatomical variables (for example 
cortical thickness and surface area), i.e. doing a vertex-wise correlation 
between 2 maps for a cohort of subjects. Maybe it is possible with the command 
line mri-glmfit and with the argument "--pvr » for per-vertex regressors? Is 
that possible or not ? If yes could i have some extra information to use 
properly the command ?
Thanks by advance,
My best,

Sophie Maingault - PhD Student 

IMN, Institut des Maladies Neurodégénératives, UMR 5293
Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université 
de Bordeaux
Université de Bordeaux
146 rue Léo Saignat - CS 61292 - Case 28
33 076 Bordeaux cedex
http://www.imn-bordeaux.org/ 





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[Freesurfer] Hippocampal subfield segmentation with T1

[Zhuang, Xiaowei]

Dear Freesurfer expert,

I am using Freesurfer V6.0 beta version to run the hippocampal subfield 
segmentation with 2 inputs, a standard T1 and a high resolution T2.

Below are the details about the 2 images.

T1: resolution: 0.8*0.8*0.8 mm,  orientation: Sagittal(S>T4.1>C-0.8)
T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5).

The instruction says in order to use both of them for hippocampal segmentation, 
T2 should be in the same orientation as T1. Therefore, the two images cannot be 
used directly.

Is it possible for me to do some reorient preprocess on the T2 image and then 
run through the segmentation?

Or is it possible to coregister the T1 into T2 space, making them both high 
resolution and run through the segmentation? Will this affect the Freesurfer 
pipeline and the final subfields output?

Any suggestion will help.

Sincerely thanks,
Xiaowei.



[Cleveland Clinic logo]


Xiaowei Zhuang   |  Research Engineer  |  Lou Ruvo Center for Brain Health
 Cleveland Clinic  |  888 W Bonneville Ave.   |  Las Vegas, NV 89106  | (702) 
685-6051




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Re: [Freesurfer] LUT in ImageJ

[Bruce Fischl]

Hi Kaiming

yes, that file should exist in $FREESURFER_HOME. Not sure about ImageJ - 
you might want to ask them

cheers
Bruce
On Wed, 16 Mar 2016, Kaiming Yin wrote:

> Dear guys,
> Is there a file of "FreeSurferColorLUT.txt" available in the Freesurfer
> folders, or should I copy/paste the texts to a .txt file directly from the
> FS website?
> 
> Also, is there a way to transform this LUT table to enable it to be loaded
> into ImageJ, or can it work directly well in ImageJ?
> 
> Thanks,
> Kaiming
> 
>
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Re: [Freesurfer] Skull strip

[Bruce Fischl]

Hi Uli

that looks like a pretty dramatic failure for the surfaces even without 
considering the skull stripping problem. There are some expert options that 
can improve this a ton (e.g. mris_make_surfaces -wlo and such). If you 
would prefer you can upload the whole subject (tarred and gzipped ) and we 
can figure out better options for you
cheers
Bruce


On Wed, 16 Mar 2016, ulrike 
kaunzner wrote:

> Hi,
> We have problems with the skull of one subjects (please see below). We tried 
> adjusting the watershed parameters, but it still did not work.
> What else can we do to change the surface?
>
> Thank you for your help!
>
> Best,
> Uli
>
>
>
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[Freesurfer] surface based analysis using FA maps

[Alshikho, Mohamad J.]

Hi Doug,
I would like to run surface based analysis using FA maps. I am not exactly sure 
that what I am doing is totally right specially step 2 . I used the following 
commands:


1.   I registered the FA maps to T1 using the command:  bbregister --s bert 
--mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat

2.   I concatenated the subject's FA maps using the command :  mris_preproc 
-target fsaverage -hemi lh -iv .bert1/dtifit_FA.nii reg.dat -iv 
bert2/dtifit_FA.nii reg.dat  --projfrac 0.5 --out lh.FA.mgz

3.   Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex 
--sval  lh.FA.mgz --tval lh.FA_5mm.mgz

4.   Then GLM analysis using mri_glmfit

5.   Correction for multiple comparison mri_glmfit-sim

Kindly, are these steps correct?
I highly appreciate any input on this!


Best,
Mohamad
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Re: [Freesurfer] group analysis all measures same results

[Kaiming Yin]

Dear Douglas,

1) Does this beta version of FS 6
(freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz) also have
problems with the individual data analysis or the volumetric group
analysis, e.g. the files in the stats/ folder for each subject?

2) So could I use the results of these surface-based group analyses after
running the "-qcache" on the latest "-dev" version
(freesurfer-Linux-centos6_x86_64-dev-20160315) available today on the
website then? I tried one data for "-qcache" with this latest -dev version,
and see the files of ?h.area.fwhm10... and ?h.thickness.fwhm10... are
different now (mri_diff), but still the same between ?h.area.fwhm10... and
?h.area.pial.fwhm10... . Is it right?

3) How about the hippocampus and brainstem sub-structure analyses, are
there changes on these features within different beta versions too?

Thanks,
Kaiming

On 15 March 2016 at 18:00, Douglas N Greve 
wrote:

>
> this only has to do with the qcache part of recon-all, so you could use
> version 5.3 recon-all -qcache and it should be fine. However, it is not a
> good idea to try to publish using the analysis from the version of FS that
> you used. That was a beta version of version 6 and things will change.
>
>
> On 03/15/2016 01:56 PM, Kaiming Yin wrote:
>
>> Dear Douglas,
>>
>> Is there anything I can do now to fix this now? I don't want to re-run
>> all the data again.
>>
>> Thanks,
>> Kaiming
>>
>>
>> On 15 March 2016 at 16:53, Douglas N Greve > > wrote:
>>
>>
>> OK, this is a bug that I found and fixed in early Nov. Sorry,
>> that's part of the danger of using a beta version.
>>
>> On 03/14/2016 12:22 PM, Kaiming Yin wrote:
>>
>> Dear Douglas,
>>
>> I re-run the "-qcache" on one data and it took 8 mins to
>> finish. Still the files are the same, all in 668.6kB size.
>>
>>
>> Kaiming
>>
>> On 14 March 2016 at 15:56, Douglas Greve
>> 
>> > >> wrote:
>>
>> I don't know what happened. I cannot replicate it here.
>> Can you
>> re-run the recon-all -s -qcache command and verify that
>> the files
>> are still the same?
>>
>>
>> On 3/14/16 11:11 AM, Kaiming Yin wrote:
>>
>> Dear Douglas,
>>
>> Yes, both of the two pairs of files are the same. i.e.
>>
>> mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
>>
>> diffcount 0
>>
>>
>> mri_diff rh.thickness.fwhm10.fsaverage.mgh
>> rh.area.fwhm10.fsaverage.mgh
>>
>> diffcount 0
>>
>>
>> Does this mean I run the "-qcache" wrongly? I just run
>> "recon-all
>> -s XX -qcache" on each subject.
>>
>> Thanks,
>> Kaiming
>>
>>
>> On 14 March 2016 at 14:58, Douglas Greve
>> > 
>> >
>> >> wrote:
>>
>> Check whether rh.ad_hv.thick.10.mgh and
>> rh.ad_hv.area.10.mgh
>> are the same, ie,
>> mri_diff  rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
>>
>> If those are the same, then check whether
>> thickness.fwhm10.fsaverage and
>> area.fwhm10.fsaverage  are the
>> same in each subject
>>
>>
>> On 3/14/16 10:53 AM, Kaiming Yin wrote:
>>
>> Dear Douglas,
>>
>> My command lines were, e.g. right thickness
>> and right white
>> surface (using the same ad_hv.fsgd and
>> group_diff.mtx files
>> in the command lines):
>>
>>
>> ad_hv.fsgd
>>
>> GroupDescriptorFile 1
>> Title AD_HV_GroupAnalysis
>> Class AD
>> Class HV
>> InputAD_003AD
>> InputAD_005AD
>> ...
>> InputHV_ABHV
>> InputHV_AEHV
>>
>>
>> group_diff.mtx
>>
>> 1 -1
>>
>>
>> right thickness
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in
>> thickness.fwhm10.fsaverage --target fsaverage
>> --hemi rh
>> --out rh.ad_hv.thick.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd
>> 

Re: [Freesurfer] Replacing / turning off denoising filter

[Falk Lüsebrink]

Hi Bruce,



I have applied one of his denoising algorithms on my high resolution datasets 
and also got very nice results. I used it on a single subject only, however, 
this could be beneficial for the upcoming hires pipeline to account for lower 
SNR.



You can find his algorithms and publications here:



https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging/mri-denoising/mri-denoising-software



Best,

Falk



Von: Bruce Fischl
Gesendet: Freitag, 18. März 2016 19:43
An: Freesurfer support list
Betreff: Re: [Freesurfer] Replacing / turning off denoising filter



that's interesting. Is it open source? If so, can you point us at it? Maybe
someone should compare it to the version I wrote 20 years ago :)

On Fri, 18 Mar 2016, Mojmír Vinkler wrote:

> Thanks!
> Just FYI - we applied newer version of NLME from Pierrick Coupé before
> running freesurfer and it greatly improved segmentation results.
>
> On Wed, Mar 16, 2016 at 3:47 PM Bruce Fischl 
> wrote:
>   Hi Mojmir
>
>   we don't apply mri_nlfilter by default so there is no need to
>   turn it
>   off. You are welcome to try it out. It implement some nonlinear
>   filters
>   including what is now called nonlocal means as described in this
>   paper:
>
> http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?reload=true=745
>   732
>
>
>   cheers
>   Bruce
>
>   On
>   Wed, 16 Mar 2016, Mojmír Vinkler wrote:
>
>   > Hi,
>   > I was wondering if it's possible to replace or turn off your
>   denoising
>   > algorithm `mri_nlfilter`. We'd like to try different denoising
>   filters and
>   > compare how they influence segmentation performance. Right now
>   we're
>   > applying filter before running recon-all, but I fear that
>   applying your
>   > filter on already filtered image might degrade our analysis.
>   >
>   > I couldn't find any mention of mri_nlfilter besides this one
>   on 
> mailinglisthttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020
>   762.
>   > html. I hope I didn't miss something anything.
>   >
>   > Thanks!
>   > Mojmir
>   >
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Re: [Freesurfer] Anterior to Posterior Length

[Heather Acuff]

Thank you very much!
Heather

On Wed, Mar 16, 2016 at 11:24 AM, Bruce Fischl 
wrote:

> I see. I don't think we generate that by default. If you have a bunch of
> subjects I guess you could great a single vertex label at the frontal pole
> and another at occipital pole on fsaverage, then map each of them to each
> subjects and compute the distance between them. That will be a rough
> estimate. Or you could transform the brainmask.mgz to tal coords and see
> what the first and last a/p coords are. Neither will be perfect
>
>
> On Wed, 16 Mar 2016, Heather Acuff wrote:
>
> Hi Bruce,
>> I'm asking for the length of the entire hemisphere.
>>
>> Thank you!
>> Heather
>>
>> On Wed, Mar 16, 2016 at 11:19 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Heather
>>
>>   the anterior/posterior length of each tract you mean? Or the
>>   length of the entire hemi?
>>   Bruce
>>   On Wed, 16 Mar 2016, Heather Acuff wrote:
>>
>> Good morning,
>>
>> I apologize if this email was sent out twice.  I
>> would like to
>> use anterior to posterior length as a covariate in
>> my DTI analysis.  Is
>> there an easy way to obtain this information for
>> each subject?
>>
>> Thank you,
>> Heather
>>
>>
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>>
>>
>>
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Re: [Freesurfer] Anterior to Posterior Length

[Bruce Fischl]

I see. I don't think we generate that by default. If you have a bunch of 
subjects I guess you could great a single vertex label at the frontal pole 
and another at occipital pole on fsaverage, then map each of them to each 
subjects and compute the distance between them. That will be a rough 
estimate. Or you could transform the brainmask.mgz to tal coords and see 
what the first and last a/p coords are. Neither will be perfect


On Wed, 16 Mar 2016, Heather Acuff wrote:


Hi Bruce,
I'm asking for the length of the entire hemisphere.

Thank you!
Heather

On Wed, Mar 16, 2016 at 11:19 AM, Bruce Fischl 
wrote:
  Hi Heather

  the anterior/posterior length of each tract you mean? Or the
  length of the entire hemi?
  Bruce
  On Wed, 16 Mar 2016, Heather Acuff wrote:

Good morning,

I apologize if this email was sent out twice.  I
would like to
use anterior to posterior length as a covariate in
my DTI analysis.  Is
there an easy way to obtain this information for
each subject?

Thank you,
Heather


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Re: [Freesurfer] mri_robust_register question

[dgw]

Hi Ji-Won,

Why not just input both T1s to recon-all it will motion correct and
average and then all of your functionals will be registered to the
same FS data?

hth
d

On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang  wrote:
> Dear. All.
>
> Hi. How are you?
>
> It might be a very naive question, but your advice is greatly appreciated!
>
> I'm trying to register 2 T1s obtained from 1 subject on different days and
> then register the functional scans to their corresponding T1s (registering
> the functional scans to the same day's T1). By doing so, I expect to get
> everything into the same space.
>
> (Each subject was scanned twice on two different days etc., day1 and day2)
>
> After running mri_robust_register onto day2's T1 as targetting day1's T1, I
> get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run
> preproc-sess(that does registration as well) onto day2's functional scans.
>
> Is there a way to make preproc-sess do register functional scans of day2 to
> v2to1.mgz(of day2 that's created by mri_robust_register), not the original
> 046.mgz?
>
> The commands that I run are:
>
> recon-all -s $SUBJECT -all
>
> mri_robust_register --mov
> /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst
> /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta
> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov
> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights
> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale
> --satit
>
> preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force
> -fwhm 0
>
> Please feel free to give me any advice!
>
> Thank you very much.
>
> Best,
> Ji Won
>
>
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Re: [Freesurfer] FreeSurfer 6.0

[Alan Francis]

Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
ran the HSF method successfully. Have they retracted that version?

best,

Alan

On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl 
wrote:

> actually there is no beta yet, but hopefully within a week or so
>
> On Wed, 16 Mar 2016, Alan Francis wrote:
>
> Hi Elizabeth:
>>
>> I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
>> Beta is available for download. Here is the URL:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>
>> best,
>>
>> Alan
>>
>> On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
>>  wrote:
>>   Dear ladies and gentlemen,
>>
>> for a research project I need to measure the volume of the different
>> hippocampus subregions. I want to use FreeSurfer 6.0 for that but I
>> can only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet
>> released and if so, when will it be released? If it is already
>> released, could you tell me where to find it?
>>
>> Thank you very much in advance.
>>
>> Kind regards,
>>
>> Elisabeth Paul
>>
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>>
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>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> --
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> Alan N. Francis PhD
>> NIDA T32  Fellow in Computational Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>
>>
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>
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> The information in this e-mail is intended only for the person to whom it
> is
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> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
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|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


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Re: [Freesurfer] FreeSurfer 6.0

[Alan Francis]

Hi Elizabeth:

I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
Beta is available for download. Here is the URL:

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

best,

Alan

On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul <
elisabeth.p...@student.uva.nl> wrote:

> Dear ladies and gentlemen,
>
> for a research project I need to measure the volume of the different
> hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can
> only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if
> so, when will it be released? If it is already released, could you tell me
> where to find it?
>
> Thank you very much in advance.
>
> Kind regards,
>
> Elisabeth Paul
>
> ___
> 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.
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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Re: [Freesurfer] aparc stats volume outputting area instead

[Clare Loane]

Hi Doug, 

I am using version 5.3 and the terminal output does not state an error (below) 
and the file is created (attached) but as you will see, it is the area 
measurements which are output. 

dcnmac75:Freesurfer clare$ aparcstats2table --subjects CON_001 CON_002 CON_003 
CON_004 CON_006 CON_007 CON_008 CON_009 CON_010 CON_011 CON_013 CON_014 CON_015 
CON_016 CON_017 CON_018 CON_019 CON_021 CON_022 CON_025 CON_026 CON_027 CON_028 
CON_029 CON_030 CON_032 CON_033 CON_034 CON_035 CON_036 CON_038 CON_039 CON_040 
CON_041 CON_042 CON_045 CON_049 CON_054 CON_055 CON_057 CON_063 OXCON_005 
OXCON_009 OXCON_012 OXCON_025 OXCON_026 OXCON_028 OXCON_029 OXCON_031 OXCON_040 
OXCON_042 OXCON_052 OXCON_053 OXCON_054 OXCON_055 OXCON_058 OXCON_059 OXCON_060 
OXCON_061 OXCON_062 OXCON_064 OXCON_065 OXCON_066 OXCON_067  --hemi rh –meas 
volume --tablefile aparc_stats_volume_rh.txt --skip 
SUBJECTS_DIR : /Users/clare/Desktop/MAP/Volumetrics/FreeSurfer/CONTROLS/
Parsing the .stats files
Building the table..
Writing the table to aparc_stats_volume_rh.txt

Since posting the original message, it does seem that the correct measurement 
can be acquired when I aparcstat2table on subjects individually. Although often 
it will state error that the rh.aparc.stats is not found or is too small to be 
a valid stats file. This is not the case as they are all there and full of 
measurements. 

Many thanks, 

Clare



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 15 March 2016 16:55
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparc stats volume outputting area instead

Can you send the terminal output? Also, what version are you using?

On 03/14/2016 09:56 AM, Clare Loane wrote:
> Hi,
>
> I am trying to pull out the volumes from the aparc stats file but when
> I input the following (below) it produces a file identical to the area
> instead:
>
> aparcstats2table --subjects 001 002 003 --hemi rh --meas volume
> --tablefile aparc_stats_volume_rh.txt
>
> It works fine for thickness and area as well aseg_stats.
>
> I would appreciate any help with this.
>
> Thank you!
>
> Clare
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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rh.aparc.area   rh_bankssts_arearh_caudalanteriorcingulate_area 
rh_caudalmiddlefrontal_area rh_cuneus_area  rh_entorhinal_area  
rh_fusiform_arearh_inferiorparietal_area
rh_inferiortemporal_arearh_isthmuscingulate_area
rh_lateraloccipital_arearh_lateralorbitofrontal_arearh_lingual_area 
rh_medialorbitofrontal_area rh_middletemporal_area  rh_parahippocampal_area 
rh_paracentral_area rh_parsopercularis_area rh_parsorbitalis_area   
rh_parstriangularis_arearh_pericalcarine_area   rh_postcentral_area 
rh_posteriorcingulate_area  rh_precentral_area  rh_precuneus_area   
rh_rostralanteriorcingulate_arearh_rostralmiddlefrontal_area
rh_superiorfrontal_area rh_superiorparietal_area
rh_superiortemporal_arearh_supramarginal_area   rh_frontalpole_area 
rh_temporalpole_arearh_transversetemporal_area  rh_insula_area  
rh_WhiteSurfArea_area
CON_001 783.0   631.0   1962.0  1329.0  333.0   2856.0  5047.0  2921.0  990.0   
5077.0  2516.0  2968.0  1671.0  3162.0  779.0   1449.0  1634.0  644.0   1495.0  
1726.0  3606.0  1014.0  4683.0  3745.0  570.0   4663.0  6534.0  5550.0  3250.0  
3836.0  223.0   492.0   296.0   2296.0  80734.1
CON_002 1015.0  612.0   2199.0  1572.0  405.0   3356.0  6356.0  2983.0  816.0   
4694.0  2154.0  2791.0  1525.0  3528.0  719.0   1300.0  1713.0  793.0   1371.0  
1313.0  4272.0  1149.0  5107.0  4136.0  565.0   5130.0  6199.0  5632.0  3581.0  
3819.0  294.0   412.0   295.0   2559.0  84361.6
CON_003 924.0   848.0   2009.0  1446.0  549.0   3182.0  4123.0  2704.0  884.0   
4135.0  2059.0 

Re: [Freesurfer] Hippocampal subfield segmentation with T1

[Bruce Fischl]

Hi Xiaowei

you can try mri_robust_register --cost nmi or --cost mi, then give the 
resulting transform to mri_convert -at transform.lta -rl T2.mgz



The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will 
have the same geometry. You can also try mri_coreg if you like instead of 
mri_robust_register if it doesn't work well


cheers
Bruce


On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote:



Dear Freesurfer expert,

 

I am using Freesurfer V6.0 beta version to run the hippocampal subfield
segmentation with 2 inputs, a standard T1 and a high resolution T2.

 

Below are the details about the 2 images.

 

T1: resolution: 0.8*0.8*0.8 mm,  orientation: Sagittal(S>T4.1>C-0.8)

T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5).

 

The instruction says in order to use both of them for hippocampal
segmentation, T2 should be in the same orientation as T1. Therefore, the two
images cannot be used directly.

 

Is it possible for me to do some reorient preprocess on the T2 image and
then run through the segmentation?

 

Or is it possible to coregister the T1 into T2 space, making them both high
resolution and run through the segmentation? Will this affect the Freesurfer
pipeline and the final subfields output?

 

Any suggestion will help.

 

Sincerely thanks,

Xiaowei.  

 

 

 

Cleveland Clinic logo

 

Xiaowei Zhuang   |  Research Engineer  |  Lou Ruvo Center for Brain
Health

 Cleveland Clinic  |  888 W Bonneville Ave.   |  Las Vegas, NV
89106  | (702) 685-6051

 

 

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Re: [Freesurfer] mri_robust_register question

[Martin Reuter]

Hi,

when using recon-all for this, the right way would be to run both images 
through the longitudinal stream. This will create a mid-space template 
and map both time points to it. That space can also be used as target 
for the functional data. That way you stay unbiased.

Probably the potential processing bias is small for this kind of 
analysis, so you can also probably get away with using the first time 
point structural space for everything. I am not familiar with the 
preproc-sess command to give advice. But there are others on this list 
who know.

Best, Martin

On 03/17/2016 03:16 PM, dgw wrote:
> Hi Ji-Won,
>
> Why not just input both T1s to recon-all it will motion correct and
> average and then all of your functionals will be registered to the
> same FS data?
>
> hth
> d
>
> On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang  wrote:
>> Dear. All.
>>
>> Hi. How are you?
>>
>> It might be a very naive question, but your advice is greatly appreciated!
>>
>> I'm trying to register 2 T1s obtained from 1 subject on different days and
>> then register the functional scans to their corresponding T1s (registering
>> the functional scans to the same day's T1). By doing so, I expect to get
>> everything into the same space.
>>
>> (Each subject was scanned twice on two different days etc., day1 and day2)
>>
>> After running mri_robust_register onto day2's T1 as targetting day1's T1, I
>> get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run
>> preproc-sess(that does registration as well) onto day2's functional scans.
>>
>> Is there a way to make preproc-sess do register functional scans of day2 to
>> v2to1.mgz(of day2 that's created by mri_robust_register), not the original
>> 046.mgz?
>>
>> The commands that I run are:
>>
>> recon-all -s $SUBJECT -all
>>
>> mri_robust_register --mov
>> /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst
>> /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta
>> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov
>> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights
>> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale
>> --satit
>>
>> preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force
>> -fwhm 0
>>
>> Please feel free to give me any advice!
>>
>> Thank you very much.
>>
>> Best,
>> Ji Won
>>
>>
>> ___
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>>
>>
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>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> 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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Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] mris_flatten error: bad vertex

[Ji Won Bang]

Dear. Freesurfer experts.

Hi.

I'm having a problem with mris_flatten (version 5.3.0)


Could you please help me fix this problem?

My command line is:
mris_flatten -w 0 -distances 12 7
$SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
$SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat

It returns the error:
using write iterations = 0
sampling 7 neighbors out to a distance of 12 mm
reading patch /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d
with 30434 vertices (20.5% of total)
MRISreadPatch: bad vertex # (148517) found in patch file
No such file or directory

When making the patch lh.oc.patch.3d, I followed the processes below:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast UpperLower

select 3 points along a boundary between upper and lower visual fields
(near calcarine sulcus) and press "Cut line". Then, select 4 points to
define the cutting plane: 1 on lower side of the line, 2 on upper side of
the line, 3 on the opposite surface (use rotation tool), and 4 to specify
which portion of surface is kept, and press "Cur plane". File->Patch->Save
Patch As lh.oc.patch.3d

So I think I made the patch correctly.

! weird thing that I suspect is that when I click save patch as, the
default location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it
to $SUBJECTS_DIR/$SUBJECT/surf

Could you please help me?

Thanks a lot!

Best,
Ji Won
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Re: [Freesurfer] Replacing / turning off denoising filter

[Bruce Fischl]

thanks Falk
Bruce
On Fri, 18 Mar 2016, Falk Lüsebrink wrote:



Hi Bruce,

 

I have applied one of his denoising algorithms on my high resolution
datasets and also got very nice results. I used it on a single subject only,
however, this could be beneficial for the upcoming hires pipeline to account
for lower SNR.

 

You can find his algorithms and publications here:

 

https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical
-imaging/mri-denoising/mri-denoising-software

 

Best,

Falk

 

Von: Bruce Fischl
Gesendet: Freitag, 18. März 2016 19:43
An: Freesurfer support list
Betreff: Re: [Freesurfer] Replacing / turning off denoising filter

 

that's interesting. Is it open source? If so, can you point us at it? Maybe
someone should compare it to the version I wrote 20 years ago :)

On Fri, 18 Mar 2016, Mojmír Vinkler wrote:

> Thanks!
> Just FYI - we applied newer version of NLME from Pierrick Coupé before
> running freesurfer and it greatly improved segmentation results.
>
> On Wed, Mar 16, 2016 at 3:47 PM Bruce Fischl 
> wrote:
>   Hi Mojmir
>
>   we don't apply mri_nlfilter by default so there is no need to
>   turn it
>   off. You are welcome to try it out. It implement some nonlinear
>   filters
>   including what is now called nonlocal means as described in this
>   paper:
>
>http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?reload=true=745

>   732
>
>
>   cheers
>   Bruce
>
>   On
>   Wed, 16 Mar 2016, Mojmír Vinkler wrote:
>
>   > Hi,
>   > I was wondering if it's possible to replace or turn off your
>   denoising
>   > algorithm `mri_nlfilter`. We'd like to try different denoising
>   filters and
>   > compare how they influence segmentation performance. Right now
>   we're
>   > applying filter before running recon-all, but I fear that
>   applying your
>   > filter on already filtered image might degrade our analysis.
>   >
>   > I couldn't find any mention of mri_nlfilter besides this one
>   
onmailinglisthttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-Octo
ber/020
>   762.
>   > html. I hope I didn't miss something anything.
>   >
>   > Thanks!
>   > Mojmir
>   >
>   >___
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>
>
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Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Hi Bruce,

Thank you very much! :) 
I think somethings wrong with gnumeric indeed just discovered that gedit 
works fine. 

As for 3, that would mean that the data are not in native space? I'm trying to 
understand this concept of "summary statistics" :-).

Thanks again in advance.

Caroline



-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 13:59
Aan: Freesurfer support list 
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
something strange with gnumeric and I'm not sure we are qualified to help you.

As for 3, the tables contain summary stats and so don't need to be mapped into 
any common space.

cheers
Bruce


On Thu, 17 Mar 2016, Caroline
Beelen wrote:

> 
> Dear FS,
> 
>  
> 
> 1. I typed: aparcstats2table --hemi lh --meas thickness --subjects 
> A01_T1
> 
> > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed 
> > by)
> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, 
> it generated the table attached. Why are the mean cortical thickness 
> values sometimes depicted wrong and how can I change this (or do I 
> need to do this by hand)?
> 
>  
> 
> 2. I noticed aparcstats2table doesn’t generate a mean volume (column 
> AJ is empty). Is that supposed to be the case?
> 
>  
> 
> 3. A final question: the aparcstats2table and asegstats2table contain 
> data in native space. Before loading Qdec data needs to be smoothed 
> onto the average subject (using qcache). As s I understand correctly 
> from your answer below and the tutorial I could either just use these 
> values to create the qdectable.dat file or just load the tables in Qdec 
> itself.
> 
> Does that mean that the values of these tables somehow (have) 
> change(d) during the smoothing process?
> 
>  
> 
> Sorry if my questions are rather basic…, but I try to fully 
> understand. J
> 
> Thanks again for responding in advance.
> 
>  
> 
> Kind regards,
> 
>  
> 
> Caroline
> 
> > 
> 
>  
> 
>  
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
> Verzonden: woensdag 16 maart 2016 15:38
> Aan: freesurfer@nmr.mgh.harvard.edu
> Onderwerp: Re: [Freesurfer] gnumeric file
> 
>  
> 
>  
> 
> On 3/16/16 6:52 AM, Caroline Beelen wrote:
>
>   Hi FS team,
>
>    
>
>   Sorry for these rather basic questions…
>
>    
>
>   I'm not sure whether the gnumeric file is an ascii file (see
>   mails below). Attached you'll find the file. It seems the case
>   when you open it in the terminal screen that the nr's look fine
>   (with command cat). However as soon as you type the command
>   gnumeric and so on, it creates a wrong table from the start (see
>   file attached). Can I somehow change this?
> 
> How did you create this file? The aparcstats2table command produces a 
> simple ascii file.
>
>    
>
>   I have an additional question:
>
>   I was looking at the Qdec info (tutorial) and I am not totally
>   sure how to create the table.dat file… Where to get the volume
>   measures from, if you’d like to include those? The statistical
>   folder (where the tables are from)?
> 
> Run asegstats2table and/or aparcstats2table to create a table of the 
> volumes, then extract the values you need. BTW, you don't have to have 
> volume measures in the qdec table.
>
>    
>
>   Thank you for responding in advance.
>
>    
>
>   Kind regards, Caroline
>
>    
>
>   -Oorspronkelijk bericht-
>
>   Van: freesurfer-boun...@nmr.mgh.harvard.edu
>   [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
>   Greve
>
>   Verzonden: dinsdag 8 maart 2016 0:24
>
>   Aan: freesurfer@nmr.mgh.harvard.edu
>
>   Onderwerp: Re: [Freesurfer] mean thickness
>
>    
>
>   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).
>
>   >
>
>  

Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

that's a good point
On Wed, 16 Mar 2016, Martin Reuter wrote:

>
> Although it should be mentioned that outputs (even of subfields) are
> going to change due to differences in the regular freesurfer processing,
> as the subfields stream builds upon the regular FS stream.
>
> Best, Martin
>
>
> On 03/16/2016 10:52 AM, Eugenio Iglesias wrote:
>> I only changed some details (e.g., temporary directories) that do not affect 
>> the output.
>>
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> - Original Message -
>> From: "Bruce Fischl" 
>> To: "Freesurfer support list" 
>> Sent: Wednesday, March 16, 2016 3:49:31 PM
>> Subject: Re: [Freesurfer] FreeSurfer 6.0
>>
>> yes, although the hippocampal stuff hasn't changed I don't think
>> (Eugenio: is that correct)?
>>
>> On Wed, 16 Mar 2016, Alan Francis wrote:
>>
>>> Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and
>>> ran the HSF method successfully. Have they retracted that version?
>>>
>>> best,
>>>
>>> Alan
>>>
>>> On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl 
>>> wrote:
>>>actually there is no beta yet, but hopefully within a week or so
>>>On Wed, 16 Mar 2016, Alan Francis wrote:
>>>
>>>  Hi Elizabeth:
>>>
>>>  I ran the Hippocampal subfields on 6.0 beta. The
>>>  parcellation looks great.
>>>  Beta is available for download. Here is the URL:
>>>
>>>  https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>>
>>>  best,
>>>
>>>  Alan
>>>
>>>  On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
>>>   wrote:
>>>Dear ladies and gentlemen,
>>>
>>>  for a research project I need to measure the volume
>>>  of the different
>>>  hippocampus subregions. I want to use FreeSurfer 6.0
>>>  for that but I
>>>  can only find FreeSurfer 5.3 online. Is FreeSurfer
>>>  6.0 not yet
>>>  released and if so, when will it be released? If it
>>>  is already
>>>  released, could you tell me where to find it?
>>>
>>>  Thank you very much in advance.
>>>
>>>  Kind regards,
>>>
>>>  Elisabeth Paul
>>>
>>>  ___
>>>  Freesurfer mailing list
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>>>
>>>
>>>  The information in this e-mail is intended only for
>>>  the person to whom
>>>  it is
>>>  addressed. If you believe this e-mail was sent to
>>>  you in error and the
>>>  e-mail
>>>  contains patient information, please contact the
>>>  Partners Compliance
>>>  HelpLine at
>>>  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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>>>
>>>
>>>
>>>  --
>>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>>
>>>  Alan N. Francis PhD
>>>  NIDA T32  Fellow in Computational Neuroscience
>>>  Brain Imaging Center
>>>  McLean Hospital
>>>  Harvard Medical School
>>>  115 Mill Street, Belmont, MA 02478
>>>  al...@bwh.harvard.edu
>>>  afran...@mclean.harvard.edu
>>>
>>>
>>>
>>>  |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>>
>>>
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> --
>>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>>
>>> Alan N. Francis PhD
>>> NIDA T32  Fellow in Computational Neuroscience
>>> Brain Imaging Center
>>> McLean Hospital
>>> Harvard Medical School
>>> 115 Mill Street, Belmont, MA 02478
>>> al...@bwh.harvard.edu
>>> 

[Freesurfer] WM edit, remove GM bright rim

[Min Liu]

Dear Freesufer users,

We have some T1 images having a rim of bright signal in the GM at some
spots like the one showing in the attached Figure 1.  The WM surface goes
out to include this bright signal and the cortex ends up artificially
thin.  We followed the standard WM edit procedure, which is to erase the
bright signal in wm.mgz. As shown in Figure 2, the bright rim is replaced
with intensity 1 (red). However, that doesn't improve the situation.  Does
anyone know a way to prevent the surface from going out?

Thanks,


-- 
Min
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Re: [Freesurfer] FreeSurfer 6.0

[Bruce Fischl]

actually there is no beta yet, but hopefully within a week or so
On Wed, 16 
Mar 2016, Alan Francis wrote:



Hi Elizabeth:

I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great.
Beta is available for download. Here is the URL:

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

best,

Alan

On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul
 wrote:
  Dear ladies and gentlemen,

for a research project I need to measure the volume of the different
hippocampus subregions. I want to use FreeSurfer 6.0 for that but I
can only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet
released and if so, when will it be released? If it is already
released, could you tell me where to find it?

Thank you very much in advance.

Kind regards,

Elisabeth Paul

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|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
                                                                            
                             
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Dear FS

I typed in: aparcstats2table --hemi lh --meas thickness --subjects A01_T1
> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed by) 
> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, it 
> generated the table attached in the previous mail.

Thank you with regards to the second question.. However, for volumes 
aparcstats2table it doesn't generate a mean volume (column AJ is empty). Is 
that supposed to be?

Kind regards,
Caroline
>

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file


On 3/16/16 6:52 AM, Caroline Beelen wrote:
Hi FS team,

Sorry for these rather basic questions...

I'm not sure whether the gnumeric file is an ascii file (see mails below). 
Attached you'll find the file. It seems the case when you open it in the 
terminal screen that the nr's look fine (with command cat). However as soon as 
you type the command gnumeric and so on, it creates a wrong table from the 
start (see file attached). Can I somehow change this?
How did you create this file? The aparcstats2table command produces a simple 
ascii file.


I have an additional question:
I was looking at the Qdec info (tutorial) and I am not totally sure how to 
create the table.dat file... Where to get the volume measures from, if you'd 
like to include those? The statistical folder (where the tables are from)?
Run asegstats2table and/or aparcstats2table to create a table of the volumes, 
then extract the values you need. BTW, you don't have to have volume measures 
in the qdec table.


Thank you for responding in advance.

Kind regards, Caroline

-Oorspronkelijk bericht-
Van: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N Greve
Verzonden: dinsdag 8 maart 2016 0:24
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] mean thickness

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





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Re: [Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Hi Bruce,

Thanks for your response. I'm using :

freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS
X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm
using:

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

Thanks in advance for your help.

best regards,
Ehsan.




On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl 
wrote:

> Hi Ehsan
>
> We need the full command line and screen output and also what your
> hardware and software environments are to help you. Certainly sounds like
> you ran out of memory though
>
> Cheers
> Bruce
>
> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon 
> wrote:
> >
> > Ehsan
>
> ___
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>
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> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Extremely small numbers of extracted pial surface area

[Karl Liu]

Dear Freesurfer experts,

 

I am reposting my question from early this week since it is not
answered. Any help much appreciated. 

 

My question is about the measure of pial surface area. Following a group
comparison and correction in QDEC, I found  a significant cluster (size: 
760mm^2) when
choosing area. pial as the measure. In order to plot group means in a bar graph,
I extract numbers from the "cache.th20.neg.y.ocn.dat" file, but the
average is less than 1. Why is the magnitude of supposed pial surface area so
small? Is this actual or standardized measure ?

 

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Re: [Freesurfer] Replacing / turning off denoising filter

[Mojmír Vinkler]

Here's another implementation
https://github.com/Inria-Visages/Anima-Public/wiki/Denoising-tools#nl-means-denoising.
We'll be comparing different methods and throw in both your and the newer
version and see if there's any significant difference at all.

On Fri, Mar 18, 2016 at 10:38 PM Bruce Fischl 
wrote:

> thanks Falk
> Bruce
> On Fri, 18 Mar 2016, Falk Lüsebrink wrote:
>
> >
> > Hi Bruce,
> >
> >
> >
> > I have applied one of his denoising algorithms on my high resolution
> > datasets and also got very nice results. I used it on a single subject
> only,
> > however, this could be beneficial for the upcoming hires pipeline to
> account
> > for lower SNR.
> >
> >
> >
> > You can find his algorithms and publications here:
> >
> >
> >
> >
> https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical
> > -imaging/mri-denoising/mri-denoising-software
> >
> >
> >
> > Best,
> >
> > Falk
> >
> >
> >
> > Von: Bruce Fischl
> > Gesendet: Freitag, 18. März 2016 19:43
> > An: Freesurfer support list
> > Betreff: Re: [Freesurfer] Replacing / turning off denoising filter
> >
> >
> >
> > that's interesting. Is it open source? If so, can you point us at it?
> Maybe
> > someone should compare it to the version I wrote 20 years ago :)
> >
> > On Fri, 18 Mar 2016, Mojmír Vinkler wrote:
> >
> > > Thanks!
> > > Just FYI - we applied newer version of NLME from Pierrick Coupé before
> > > running freesurfer and it greatly improved segmentation results.
> > >
> > > On Wed, Mar 16, 2016 at 3:47 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > > wrote:
> > >   Hi Mojmir
> > >
> > >   we don't apply mri_nlfilter by default so there is no need to
> > >   turn it
> > >   off. You are welcome to try it out. It implement some nonlinear
> > >   filters
> > >   including what is now called nonlocal means as described in this
> > >   paper:
> > >
> > >
> http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?reload=true=745
> >
> > >   732
> > >
> > >
> > >   cheers
> > >   Bruce
> > >
> > >   On
> > >   Wed, 16 Mar 2016, Mojmír Vinkler wrote:
> > >
> > >   > Hi,
> > >   > I was wondering if it's possible to replace or turn off your
> > >   denoising
> > >   > algorithm `mri_nlfilter`. We'd like to try different denoising
> > >   filters and
> > >   > compare how they influence segmentation performance. Right now
> > >   we're
> > >   > applying filter before running recon-all, but I fear that
> > >   applying your
> > >   > filter on already filtered image might degrade our analysis.
> > >   >
> > >   > I couldn't find any mention of mri_nlfilter besides this one
> > >   onmailinglisthttps://
> mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-Octo
> > ber/020
> > >   762.
> > >   > html. I hope I didn't miss something anything.
> > >   >
> > >   > Thanks!
> > >   > Mojmir
> > >   >
> > >   >___
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> > >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
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Re: [Freesurfer] WM edit, remove GM bright rim

[Bruce Fischl]

Hi Min

that looks like it might be a normalization problem. Can you post the 
orig.mgz and see what it looks like? Is there a bright rim in it also?


cheers
Bruce
On 
Wed, 16 Mar 2016, Min Liu wrote:



Dear Freesufer users,
We have some T1 images having a rim of bright signal in the GM at some spots
like the one showing in the attached Figure 1.  The WM surface goes out to
include this bright signal and the cortex ends up artificially thin.  We
followed the standard WM edit procedure, which is to erase the bright signal
in wm.mgz. As shown in Figure 2, the bright rim is replaced with intensity 1
(red). However, that doesn't improve the situation.  Does anyone know a way
to prevent the surface from going out?

Thanks,


--
Min

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Re: [Freesurfer] mri_robust_register question

[Ji Won Bang]

Hi. Daniel.

How are you?

Thanks for your reply.

That should be another option for me!

Thanks,
Ji Won

2016-03-17 15:16 GMT-04:00 dgw :

> Hi Ji-Won,
>
> Why not just input both T1s to recon-all it will motion correct and
> average and then all of your functionals will be registered to the
> same FS data?
>
> hth
> d
>
> On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang  wrote:
> > Dear. All.
> >
> > Hi. How are you?
> >
> > It might be a very naive question, but your advice is greatly
> appreciated!
> >
> > I'm trying to register 2 T1s obtained from 1 subject on different days
> and
> > then register the functional scans to their corresponding T1s
> (registering
> > the functional scans to the same day's T1). By doing so, I expect to get
> > everything into the same space.
> >
> > (Each subject was scanned twice on two different days etc., day1 and
> day2)
> >
> > After running mri_robust_register onto day2's T1 as targetting day1's
> T1, I
> > get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run
> > preproc-sess(that does registration as well) onto day2's functional
> scans.
> >
> > Is there a way to make preproc-sess do register functional scans of day2
> to
> > v2to1.mgz(of day2 that's created by mri_robust_register), not the
> original
> > 046.mgz?
> >
> > The commands that I run are:
> >
> > recon-all -s $SUBJECT -all
> >
> > mri_robust_register --mov
> > /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst
> > /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta
> > /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov
> > /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights
> > /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz
> --iscale
> > --satit
> >
> > preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force
> > -fwhm 0
> >
> > Please feel free to give me any advice!
> >
> > Thank you very much.
> >
> > Best,
> > Ji Won
> >
> >
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Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix

[Marie Schaer]

Hi Marco,

It’s pretty strange because from the recon-all.log you sent, the first LGI 
process went fine (line 14584 and 19329 for the right and left hemispheres, on 
Dec 15). Then you don’t run anything else on the surfaces and just reprocess 
the exact same LGI process for the same subject (Dec 18), and you get different 
values from what you just had, with many values <1, plus it gets stuck.

Could that be related to your change on line 51 in make_outer_surface? When you 
say misalignment, do you mean in freeview or tkmedit? Because we saw some 
occurrences of misalignment in freeview, which indeed are related to the 
surface format and as long as the surfaces align well in tkmedit then you 
should definitely not change anything in the make_outer_surface code.

Keep me posted,

Marie


On 16 Mar 2016, at 02:51, Marco Bucci 
> wrote:

Dear all,

I forward again my original post.
I also attach the recon-all.log of one of the several faulty cases.

I run freesurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0)
 in Mac OS X 10.9.4 and -lgI option with Matlab_R2013a
and I have fixed the SearchProjectionOnPial.m.

I also had to fix line 51 of make_outer_surface.m
"v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the different 
orientation"
with
"v2=[vol.vox2ras1(1,4)-v(:,1) v(:,3)+vol.vox2ras1(2,4) 
vol.vox2ras1(3,4)-v(:,2)];"
in order to use the image coordinate to fix surface orientation and alignment.

If I would use the original line 51, the surface produced by recon -lgi results
misaligned with the reference pial and image.

My problems remains the aberrantly high lgI value in most of my subject images.

Can you help me?

Yours,
Marco Bucci


-- Forwarded message --
From: Marco Bucci >
Date: 2015-12-22 23:49 GMT+02:00
Subject: Re: [Freesurfer] lGI value is aberrantly high
To: "freesurfer@nmr.mgh.harvard.edu" 
>


Dear all,

I have a problem with the LGI module.
At the step when the software computes the LGIs for the vertices,
In one vertex the lGI results aberrantly high and the software exits
with ERRORS.

I tried the solution suggested by Marie Schaer to rereconstruct
The images with "randomness"
Recon-all -autorecon2-wm -randomness -autorecon3

I tried this fix on two of my subjects
With errors. Not all subject resulted
Errors in the computation of the gyrification.

Can you help me?

Marco Bucci
Turku Pet Center

Sent from my iPhone



--

Marco Bucci, PhD in
Clinical Physiology and Nuclear Medicine
Turku PET Centre
Turku University Central Hospital (TUCH)
PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland
tel. +358 2 3132798
fax. +358 2 2318191
mobile: +358 40 6873976
UTU e-mail: mar...@utu.fi

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Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Hi Bruce,

Ok, very clear. Thank you! :-)

Regards, Caroline

-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 15:47
Aan: Freesurfer support list 
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

the data are in native space. Summary statistics means e.g. the volume of the 
left hippocampus. You don't need any registration algorithm for this type of 
thing - you just tabulate it across subjects

cheers
Bruce


On Thu, 17 Mar 2016, Caroline Beelen wrote:

> Hi Bruce,
>
> Thank you very much! :)
> I think somethings wrong with gnumeric indeed just discovered that gedit 
> works fine.
>
> As for 3, that would mean that the data are not in native space? I'm trying 
> to understand this concept of "summary statistics" :-).
>
> Thanks again in advance.
>
> Caroline
>
>
>
> -Oorspronkelijk bericht-
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
> Verzonden: donderdag 17 maart 2016 13:59
> Aan: Freesurfer support list 
> Onderwerp: Re: [Freesurfer] gnumeric file
>
> Hi Caroline
>
> have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
> something strange with gnumeric and I'm not sure we are qualified to help you.
>
> As for 3, the tables contain summary stats and so don't need to be mapped 
> into any common space.
>
> cheers
> Bruce
>
>
> On Thu, 17 Mar 2016, Caroline
> Beelen wrote:
>
>>
>> Dear FS,
>>
>>  
>>
>> 1. I typed: aparcstats2table --hemi lh --meas thickness --subjects
>> A01_T1
>>
>>> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed
>>> by)
>> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, 
>> it generated the table attached. Why are the mean cortical thickness 
>> values sometimes depicted wrong and how can I change this (or do I 
>> need to do this by hand)?
>>
>>  
>>
>> 2. I noticed aparcstats2table doesn’t generate a mean volume (column 
>> AJ is empty). Is that supposed to be the case?
>>
>>  
>>
>> 3. A final question: the aparcstats2table and asegstats2table contain 
>> data in native space. Before loading Qdec data needs to be smoothed 
>> onto the average subject (using qcache). As s I understand correctly 
>> from your answer below and the tutorial I could either just use these 
>> values to create the qdectable.dat file or just load the tables in Qdec 
>> itself.
>>
>> Does that mean that the values of these tables somehow (have)
>> change(d) during the smoothing process?
>>
>>  
>>
>> Sorry if my questions are rather basic…, but I try to fully 
>> understand. J
>>
>> Thanks again for responding in advance.
>>
>>  
>>
>> Kind regards,
>>
>>  
>>
>> Caroline
>>
>>>  
>>
>>  
>>
>>  
>>
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
>> Verzonden: woensdag 16 maart 2016 15:38
>> Aan: freesurfer@nmr.mgh.harvard.edu
>> Onderwerp: Re: [Freesurfer] gnumeric file
>>
>>  
>>
>>  
>>
>> On 3/16/16 6:52 AM, Caroline Beelen wrote:
>>
>>   Hi FS team,
>>
>>    
>>
>>   Sorry for these rather basic questions…
>>
>>    
>>
>>   I'm not sure whether the gnumeric file is an ascii file (see
>>   mails below). Attached you'll find the file. It seems the case
>>   when you open it in the terminal screen that the nr's look fine
>>   (with command cat). However as soon as you type the command
>>   gnumeric and so on, it creates a wrong table from the start (see
>>   file attached). Can I somehow change this?
>>
>> How did you create this file? The aparcstats2table command produces a 
>> simple ascii file.
>>
>>    
>>
>>   I have an additional question:
>>
>>   I was looking at the Qdec info (tutorial) and I am not totally
>>   sure how to create the table.dat file… Where to get the volume
>>   measures from, if you’d like to include those? The statistical
>>   folder (where the tables are from)?
>>
>> Run asegstats2table and/or aparcstats2table to create a table of the 
>> volumes, then extract the values you need. BTW, you don't have to 
>> have volume measures in the qdec table.
>>
>>    
>>
>>   Thank you for responding in advance.
>>
>>    
>>
>>   Kind regards, Caroline
>>
>>    
>>
>>   -Oorspronkelijk bericht-
>>
>>   Van: freesurfer-boun...@nmr.mgh.harvard.edu
>>   [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
>>   Greve
>>
>>   Verzonden: dinsdag 8 maart 2016 0:24
>>
>>   Aan: freesurfer@nmr.mgh.harvard.edu
>>
>>   Onderwerp: Re: [Freesurfer] mean thickness
>>
>>    
>>
>>   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 

Re: [Freesurfer] Reading values from overlays with PETcoreg

[Elijah Mak]

Dear Doug,

Is it possible to use BP SUVR PET that have been registered to T1 for this
gtmseg workflow? You mentioned that the mean TAC should be used as the
input. 2 quick questions: What's mean TAC and why?

Thanks.

Best Wishes,
Elijah
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[Freesurfer] mri_glmfit

[John Anderson]

Hi Experts,

What is the meaning of this error as an output of the command mri_glmfit

 

Found 0 voxels in mask
ERROR: no voxels found in the mask
  make sure at least one voxel has a non-zero value for each input
 

in other words what are therrors that can lead to such like error message

 

 

Bests,
John 
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Re: [Freesurfer] tksurfer

[Trisanna Sprung-Much]

Hi John

I do not know anything about the error that you are getting but I was also
having some problems with tksurfer and was told by Dr. Fischl that this
viewer is no longer being updated and that it would be best to try
freeview. Did you give this a go?

best wishes

Trisanna

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


On Wed, Mar 16, 2016 at 9:43 AM, John Anderson 
wrote:

> Dear experts,
> I am running into a trouble visualizing my data in tksurfer. I highly
> appreciate any advice that can help!
> I ran group analysis between two groups using GLM analysis (mri_glmfit)
> and I corrected the results for multiple comparison using
> (mri_glmfit-sim), then I ran this command to visualize the results:
>
> tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh
>
> The result attached. In my summary file I see that I have significant
> differnce only in the precentral gyrus. But the results in tksurger is not
> showing precentral gyrus. I tried to play with the thresholds and nothing
> changed.
>
> Any advice is highly appreciated!!
> Bests,
> John
>
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[Freesurfer] Post-doctoral position available – Human Neurocognitive Aging

[Arnold Bakker]

Post-doctoral position – Human Neurocognitive Aging

The Johns Hopkins University School of Medicine, Department of Psychiatry
and Behavioral Sciences, Division of Psychiatric Neuroimaging (PI: Arnold
Bakker, Ph.D.) has a vacancy for 1-2 postdoctoral scholars to perform
federally-funded research in the areas of learning and memory, aging,
dementia and depression using human functional neuroimaging methods. As
part of the research team, the candidate will be responsible for the design
and implementation of behavioral and imaging experiments aimed at assessing
learning and memory performance, or the effects of depression on learning
and memory and cognition, broadly in both young and older adults and in
individuals with memory complaints or mild cognitive impairment. Our
studies focus primarily on the role of the medial temporal lobe and
particularly the hippocampus in memory function, age- and disease-related
memory impairment and neuropsychiatric conditions. We are also interested
in neural network approaches to learning and memory, cognitive aging and
intervention using studies of resting state activity and functional
connectivity.

The Division of Psychiatric Neuroimaging is affiliated with the Johns
Hopkins Alzheimer’s Disease Research Center (JHADRC), the Division of
Geriatric Psychiatry and Neuropsychiatry, the Kirby Center for Brain
Imaging, the Center for Imaging Science (CIS) and the HOPE4MCI study. These
affiliations and the Johns Hopkins community in general provide a rich and
unique environment for collaboration and education for candidates
interested in learning and memory in aging and disease, and
neuropsychiatry.

The successful candidate will have a strong background in cognitive
neuroscience and will have significant experience with functional MRI, as
well as a background in learning and memory. A Ph.D. in Neuroscience,
Cognitive Science or Psychology is required. The successful candidate
should also have excellent writing and communication skills and be willing
to learn new MRI analysis methods. Salary will be dependent on the
experience of the individual candidate.
To be considered, please send a letter of interest including a brief
description of research interests, a curriculum vitae including a record of
research accomplishments, and the names of three professional references to
Dr. Arnold Bakker (abak...@jhu.edu).




--
Arnold Bakker, Ph.D.
Division of Psychiatric NeuroImaging
Department of Psychiatry and Behavioral Sciences
The Johns Hopkins University School of Medicine
600 N. Wolfe Street / Phipps 300
Baltimore, MD 21287
Phone: 410-502-6944 | Fax: 410-614-3676
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Re: [Freesurfer] error while running dt-recon all

[Douglas N Greve]

No, I mean that when the command is run, it will print a lot of text to 
the screen. I want to know what that text is. You can run the following 
command and send me the dng.log file

dt_recon --debug --i DTI.nii.gz --s 40 --o 
/Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log





On 03/16/2016 11:35 AM, Jasmin Alves wrote:
> Do you mean, what ends up happening? I have attached a screen shot of 
> what files are made.
>
>
>
> On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve 
> > wrote:
>
> Can you send me what dt_recon prints to the screen when your run
> the command below?
>
>
> On 3/15/16 11:40 PM, Jasmin Alves wrote:
>>
>> Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s
>> 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40
>>
>> INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/
>>
>> dt_recon logfile
>>
>> Tue Mar 15 20:37:35 PDT 2016
>>
>> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
>>
>> setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/
>>
>> cd /Users/jasminalves/Desktop/data/40
>>
>> /Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
>> /Users/jasminalves/Desktop/data/FREESURFER/40
>>
>> Jasmins-MacBook-Pro.local
>>
>> jasminalves
>>
>> /Applications/Utilities/fsl/bin/eddy_correct
>>
>> ECRefTP 0
>>
>> #@#---
>>
>> Converting input
>>
>> Tue Mar 15 20:37:35 PDT 2016
>>
>> cd /Users/jasminalves/Desktop/data/40
>>
>> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>>
>> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>>
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>
>> reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...
>>
>> TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00
>>
>> i_ras = (-0.29, 0.0116015, -0.00282784)
>>
>> j_ras = (0.0115984, 0.32, 0.00109136)
>>
>> k_ras = (-0.00284031, -0.00105848, 0.95)
>>
>> writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...
>>
>> cd /Users/jasminalves/Desktop/data/40
>>
>> mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>>
>> Jasmins-MacBook-Pro:40 jasminalves$
>>
>>
>>
>> On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve
>> > wrote:
>>
>> Can you send the full terminal output from when you run
>> dt_recon with
>> the nifti as input?
>>
>> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
>> > How was DTI.nii.gz created? DTI.nii.gz was converted from
>> the raw
>> > dicom data using dcm2nii.
>> >
>> > Response for: "What happens if you run mri_info DTI.nii.gz"
>> >
>> > Volume information for DTI.nii.gz
>> >
>> >   type: nii
>> >
>> > dimensions: 128 x 128 x 70 x 65
>> >
>> >voxel sizes: 2., 2., 2.
>> >
>> >   type: FLOAT (3)
>> >
>> >fov: 256.000
>> >
>> >dof: 0
>> >
>> > xstart: -128.0, xend: 128.0
>> >
>> > ystart: -128.0, yend: 128.0
>> >
>> > zstart: -70.0, zend: 70.0
>> >
>> > TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec,
>> flip
>> > angle: 0.00 degrees
>> >
>> >nframes: 65
>> >
>> >PhEncDir: UNKNOWN
>> >
>> > ras xform present
>> >
>> > xform info: x_r =  -0., y_r =   0.0116, z_r = 
>> -0.0028, c_r =
>> >   -0.4290
>> >
>> >   : x_a =   0.0116, y_a =   0., z_a = 
>> -0.0011, c_a =
>> > 4.1548
>> >
>> >   : x_s =  -0.0028, y_s =   0.0011, z_s = 
>>  1., c_s =
>> >   30.9622
>> >
>> > Orientation   : LAS
>> >
>> > Primary Slice Direction: axial
>> >
>> > voxel to ras transform:
>> >
>> >-1.   0.0232 -0.0057   126.2761
>> >
>> > 0.0232   1. -0.0021  -125.2474
>> >
>> >-0.0057   0.0022 2.   -38.8153
>> >
>> > 0.   0. 0. 1.
>> >
>> > voxel-to-ras determinant -8
>> >
>> > ras to voxel transform:
>> >
>> >-0.5000   0.0058 -0.001463.8052
>> >
>> > 0.0058   0.5000 0.000561.9083
>> >
>> >

Re: [Freesurfer] gnumeric file

[Bruce Fischl]

Hi Caroline

have you looked at the  lh.aparc.thickness.table? If it is correct then it 
is something strange with gnumeric and I'm not sure we are qualified to 
help you.


As for 3, the tables contain summary stats and so don't need to be mapped 
into any common space.


cheers
Bruce


On Thu, 17 Mar 2016, Caroline 
Beelen wrote:




Dear FS,

 

1. I typed: aparcstats2table --hemi lh --meas thickness --subjects A01_T1

> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed by)
gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, it
generated the table attached. Why are the mean cortical thickness values
sometimes depicted wrong and how can I change this (or do I need to do this
by hand)?

 

2. I noticed aparcstats2table doesn’t generate a mean volume (column AJ is
empty). Is that supposed to be the case?

 

3. A final question: the aparcstats2table and asegstats2table contain data
in native space. Before loading Qdec data needs to be smoothed onto the
average subject (using qcache). As s I understand correctly from your answer
below and the tutorial I could either just use these values to create the
qdectable.dat file or just load the tables in Qdec itself.

Does that mean that the values of these tables somehow (have) change(d)
during the smoothing process?

 

Sorry if my questions are rather basic…, but I try to fully understand. J

Thanks again for responding in advance.

 

Kind regards,

 

Caroline

> 

 

 

Van: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file

 

 

On 3/16/16 6:52 AM, Caroline Beelen wrote:

  Hi FS team,

   

  Sorry for these rather basic questions…

   

  I'm not sure whether the gnumeric file is an ascii file (see
  mails below). Attached you'll find the file. It seems the case
  when you open it in the terminal screen that the nr's look fine
  (with command cat). However as soon as you type the command
  gnumeric and so on, it creates a wrong table from the start (see
  file attached). Can I somehow change this?

How did you create this file? The aparcstats2table command produces a simple
ascii file.

   

  I have an additional question:

  I was looking at the Qdec info (tutorial) and I am not totally
  sure how to create the table.dat file… Where to get the volume
  measures from, if you’d like to include those? The statistical
  folder (where the tables are from)?

Run asegstats2table and/or aparcstats2table to create a table of the
volumes, then extract the values you need. BTW, you don't have to have
volume measures in the qdec table.

   

  Thank you for responding in advance.

   

  Kind regards, Caroline

   

  -Oorspronkelijk bericht-

  Van: freesurfer-boun...@nmr.mgh.harvard.edu
  [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
  Greve

  Verzonden: dinsdag 8 maart 2016 0:24

  Aan: freesurfer@nmr.mgh.harvard.edu

  Onderwerp: Re: [Freesurfer] mean thickness

   

  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

   




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