Re: [Freesurfer] visualizing paths stats by voxel

[Janosch Linkersdörfer]

Hi Anastasia and list,

sorry, I just now got around to testing out the new build of dmri_paths you 
sent me. Sadly, the results look about the same:



Here the path stats file for the left SLFt:
#!ascii label
53
1 -50.1205 2.05458 20.1324 0
2 -49.0568 1.40645 20.8743 0
3 -47.024 0.495407 22.0052 0
4 -46.0977 -0.262421 22.1583 0
5 -44.4218 -1.30921 22.7764 0
6 -43.2968 -1.3833 23.3134 0
7 -41.2815 -1.94728 24.0532 0
8 -40.1774 -2.62188 24.8471 0
9 -39.143 -3.68113 25.4572 0
10 -38.0383 -4.9254 26.3159 0
11 -37.2828 -6.68602 27.0788 0
12 -36.5155 -8.22572 27.6033 0
13 -35.7584 -10.1152 28.2235 0
14 -35.3687 -11.6727 28.7698 0
15 -34.7487 -13.5948 29.3084 0
16 -34.0861 -15.8398 29.7752 0
17 -33.9133 -17.4602 30.2452 0
18 -33.5104 -19.6399 30.5545 0
19 -33.3487 -21.7044 30.7416 0
20 -32.9916 -23.9215 30.9002 0
21 -31.4122 -26.7961 31.088 0
22 -31.2762 -28.9119 31.2611 0
23 -31.1289 -31.2752 30.8061 0
24 -30.8814 -33.1307 30.5293 0
25 -29.5803 -36.1004 30.7024 0
26 -27.2789 -39.691 31.0453 0
27 -16.641 -48.8283 35.0155 0
28 -16.5297 -49.7169 34.264 0
29 -16.5432 -50.9074 32.951 0
30 -16.7235 -51.6755 31.9552 0
31 -16.9983 -52.2055 30.3891 0
32 -17.3004 -52.6851 28.9923 0
33 -17.6197 -53.0619 27.5988 0
34 -17.9982 -53.2888 26.4068 0
35 -18.4567 -53.4429 25.1512 0
36 -18.9968 -53.6854 23.6134 0
37 -19.8229 -53.7862 21.8063 0
38 -20.4389 -54.1143 20.5701 0
39 -21.1905 -54.2719 19.3752 0
40 -21.7858 -54.4113 18.3986 0
41 -23.0093 -54.3412 16.9705 0
42 -24.1073 -54.5756 15.7345 0
43 -25.302 -54.5493 14.8829 0
44 -26.706 -54.7199 13.7208 0
45 -27.1493 -55.0881 13.003 0
46 -28.5131 -55.2495 12.4195 0
47 -25.8897 -58.0703 15.0856 0
48 -22.3874 -60.6226 18.735 0
49 -14.1178 -65.6153 25.9802 0
50 -9.17648 -68.7466 30.4727 0
51 3.31329 -77.2664 41.7526 0
52 22.0756 -89.6051 55.8685 0
53 19.4398 -88.1799 54.2416 0


What could be the problem?! I think I did what you suggested:

- install the new version of dmri_paths 
(https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it 
executable
- rerun trac-all -path for the subjects with only one time point
- rerun trac-all -stat for all subjects

Also: Is that problem only a visualization problem, or does it also mean that 
the values I get for a participant at a specific part of a tract are not 
aligned and I cannot analyze the data in that way?

Thanks for your help!!

Best,

Janosch


> On 20 Aug 2015, at 21:35, Anastasia Yendiki  
> wrote:
> 
> 
> Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of 
> dmri_paths tomorrow. You'll have to replace your copy of 
> $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" only 
> for the subjects that have 1 time point. Then rerun "trac-all -stat" with all 
> subjects together. And then tell us what other problem you find :)
> 
> Best,
> a.y
> 
> On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote:
> 
>> Hey Anastasia,
>> 
>>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki 
>>> :
>>> 
>>> 
>>> Hi Janosch - There is a bug in how the output paths are saved when 
>>> longitudinal TRACULA is run with one time point only. I'm working on a fix.
>> 
>> OK, then I'm relieved that it isn't an error on my side. Thank you very much 
>> for looking into it!
>> 
>>> In the meantime, you can try your analysis with the subjects that have 
>>> multiple time points and you won't be affected by this problem. I can see 
>>> that the subjects with a single time point are about 1/3 of your sample, 
>>> and so you may not want to drop them completely.
>> 
>> Yeah, it's children's data, so I'm happy about every measurement we got. 
>> I'll be waiting for the fixed script to be able to include all subjects in 
>> the analysis...
>> 
>>> 
>>> Thank you for trying things that nobody else has tried and finding these 
>>> bugs!
>> 
>> Somebody has to be the first, eh? :)
>> 
>> Thank you very much,
>> 
>> Janosch
>> 
>>> 
>>> More soon,
>>> a.y
>>> 
>>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote:
>>> 
 Hey Anastasia,
 
 thanks for looking into this.
 
> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki 
> :
> 
> 
> Hi Janosch - Looking at the stats files of your subjects, just by a quick 
> count of the number of lines, I see that there are some subjects that 
> have only 1 time point and some that have multiple time points, and that 
> the pathstats.byvoxel.txt files have different lengths between those two 
> types of subjects.
> 
> I suspect that the strange average path that you get has to do with how 
> this mixing of subjects was done. Did you run the subjects with a single 
> time point through the longitudinal stream as well?
 
 Yes, I ran the longitudinal stream for all subjects, also for the ones 
 with only one time point.
 
 Thanks,
 
 Janosch
 
> 
> Best,
> a.y
> 
> On Sun, 9 Aug 

Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

[Razlighi, Qolamreza R.]

Thanks again
--
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University

Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/

On Nov 3, 2015, at 9:59 AM, Bruce Fischl 
> wrote:

Hi Ray

I would assume that they are in "tkras" space, which is still "native" but is 
not voxel coords.

cheers
Bruce


On Tue, 3 Nov 2015, Razlighi, Qolamreza R. wrote:

Thanks Bruce, I read in another post that these coordinates in ascii file
are in native space. So if I load the original volume in another
visualization tool (e.g. fslview), these coordinates should be right on the
border of white/gray matter. Is that correct?
I already checked couple of them but wanted to be sure this is the case.
Also, if freeview doesn’t get the header information from ascii files, what
header info (probably a default one) it uses to plot them? Is there any way
we can give those header information separately to freeview?
Best
--
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University
Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/
On Nov 2, 2015, at 10:02 AM, Bruce Fischl 
>
wrote:

 Hi Ray

 the ascii format is pretty barebones and doesn't have e.g.
 ras2vox info
 that freeview uses to display the surfaces properly.  It's for
 ease of
 conversion and such.

 cheers
 Bruce

 On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote:

   Hi Guys,
   Why converting a surface to .asc format changes its
   spatial orientation? Specifically, I have converted
   lh.while to lh.white.asc (using: mris_convert
   lh.white lh.white.asc) and plot both of them using
   freeview but they are not corresponding. In fact,
   lh.white corresponds to the volume image (e.g
   orig.mgz) but the lh.white.asc doesn't. See the
   attached screenshot. The red curve is the
   lh.white.asc.
   Any explanation would be greatly appreciated.

   Best

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Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

[Bruce Fischl]

Hi Ray

I would assume that they are in "tkras" space, which is still "native" but 
is not voxel coords.


cheers
Bruce


On Tue, 3 Nov 2015, 
Razlighi, Qolamreza R. wrote:



Thanks Bruce, I read in another post that these coordinates in ascii file
are in native space. So if I load the original volume in another
visualization tool (e.g. fslview), these coordinates should be right on the
border of white/gray matter. Is that correct?
I already checked couple of them but wanted to be sure this is the case.
Also, if freeview doesn’t get the header information from ascii files, what
header info (probably a default one) it uses to plot them? Is there any way
we can give those header information separately to freeview?

Best

-- 
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University

Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/

On Nov 2, 2015, at 10:02 AM, Bruce Fischl 
wrote:

  Hi Ray

  the ascii format is pretty barebones and doesn't have e.g.
  ras2vox info
  that freeview uses to display the surfaces properly.  It's for
  ease of
  conversion and such.

  cheers
  Bruce

  On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote:

Hi Guys,
Why converting a surface to .asc format changes its
spatial orientation? Specifically, I have converted
lh.while to lh.white.asc (using: mris_convert
lh.white lh.white.asc) and plot both of them using
freeview but they are not corresponding. In fact,
lh.white corresponds to the volume image (e.g
orig.mgz) but the lh.white.asc doesn't. See the
attached screenshot. The red curve is the
lh.white.asc.
Any explanation would be greatly appreciated.

Best


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[Freesurfer] comparison of subcortical volume with 1.5 T and 3T...

[Gonzalo Rojas Costa]

Hi:

  I have some longitudinal study of a patient with 1.5 T images...
now, we have 3T mprage images of the same patient... how can I do the
comparison of the subcortical volume of the patient ?...

  Sincerely,


Gonzalo Rojas Costa

-- 
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

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[Freesurfer] zcat issue, lGI processing

[Andrews, Derek]

Hello Freesurfer Support Team,

I have encountered an issue running recon-all -lgi that I believe is due to a 
zcat issue on mac OSx where a .Z is added to the end of the file name the 
resulting error looks like this...

>> reading filled volume...

zcat: can't stat: 
/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 
(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z):
 No such file or directory


Upon reading through some message boards it appears replacing zcat with gzcat 
can solve this issue, however I am unsure where this troublesome zcat command 
is (it does not appear in the mriscomputelgi script).


Any suggestions or work throughs would be appreciated.


Best, Derek




Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk

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[Freesurfer] subfields segmentation FS v6.0

[Daniele Orlandi]

Dear all
I'm running the new pipleline for hippocampal subfields segmentation with
FreeSurfer v6.0 on a T13D image. As results i can extract values for the
Whole hippocampus and the following subfields: Hippocampal_tail, subiculum,
CA1, hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP,
GC-ML-DG, CA3, CA4, fimbria, HATA but not for Alveus as reported in the
paper of Iglesias, JE. et al. 2015. Was my computation wrong?

Best,
Daniele
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Re: [Freesurfer] subfields segmentation FS v6.0

[Eugenio Iglesias]

Ciao, Daniele, 
the alveus segmentation was very thin and unreliable, so we left it our of the 
results (even though it is still used in the model, and influences the fit of 
the atlas to the MRI scan). 
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 


From: "Daniele Orlandi"  
To: "Freesurfer support list"  
Sent: Tuesday, November 3, 2015 12:36:30 PM 
Subject: [Freesurfer] subfields segmentation FS v6.0 

Dear all 
I'm running the new pipleline for hippocampal subfields segmentation with 
FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole 
hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, 
hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP, GC-ML-DG, 
CA3, CA4, fimbria, HATA but not for Alveus as reported in the paper of 
Iglesias, JE. et al. 2015. Was my computation wrong? 

Best, 
Daniele 

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properly 
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Re: [Freesurfer] visualizing paths stats by voxel

[Daniele Orlandi]

Dear all
I'm running the new pipleline for hippocampal subfields segmentation with
FreeSurfer v6.0 on a T13D image. As results i can extract values for the
Whole hippocampus and the following subfields: Hippocampal_tail, subiculum,
CA1, hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP,
GC-ML-DG, CA3, CA4, fimbria, HATA but not for Alveus as reported in the
paper of Iglesias, JE. et al. 2015. Was my computation wrong?

Best,
Daniele


2015-11-03 9:37 GMT+01:00 Janosch Linkersdörfer :

> Hi Anastasia and list,
>
> sorry, I just now got around to testing out the new build of dmri_paths
> you sent me. Sadly, the results look about the same:
>
>
>
>
> Here the path stats file for the left SLFt:
>
>
>
> What could be the problem?! I think I did what you suggested:
>
> - install the new version of dmri_paths (
> https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it
> executable
> - rerun trac-all -path for the subjects with only one time point
> - rerun trac-all -stat for all subjects
>
> Also: Is that problem only a visualization problem, or does it also mean
> that the values I get for a participant at a specific part of a tract are
> not aligned and I cannot analyze the data in that way?
>
> Thanks for your help!!
>
> Best,
>
> Janosch
>
>
> > On 20 Aug 2015, at 21:35, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
> >
> >
> > Hi Janosch - Indeed, someone has to be first. I'll send you a fresh
> build of dmri_paths tomorrow. You'll have to replace your copy of
> $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path"
> only for the subjects that have 1 time point. Then rerun "trac-all -stat"
> with all subjects together. And then tell us what other problem you find :)
> >
> > Best,
> > a.y
> >
> > On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote:
> >
> >> Hey Anastasia,
> >>
> >>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu>:
> >>>
> >>>
> >>> Hi Janosch - There is a bug in how the output paths are saved when
> longitudinal TRACULA is run with one time point only. I'm working on a fix.
> >>
> >> OK, then I'm relieved that it isn't an error on my side. Thank you very
> much for looking into it!
> >>
> >>> In the meantime, you can try your analysis with the subjects that have
> multiple time points and you won't be affected by this problem. I can see
> that the subjects with a single time point are about 1/3 of your sample,
> and so you may not want to drop them completely.
> >>
> >> Yeah, it's children's data, so I'm happy about every measurement we
> got. I'll be waiting for the fixed script to be able to include all
> subjects in the analysis...
> >>
> >>>
> >>> Thank you for trying things that nobody else has tried and finding
> these bugs!
> >>
> >> Somebody has to be the first, eh? :)
> >>
> >> Thank you very much,
> >>
> >> Janosch
> >>
> >>>
> >>> More soon,
> >>> a.y
> >>>
> >>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote:
> >>>
>  Hey Anastasia,
> 
>  thanks for looking into this.
> 
> > Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu>:
> >
> >
> > Hi Janosch - Looking at the stats files of your subjects, just by a
> quick count of the number of lines, I see that there are some subjects that
> have only 1 time point and some that have multiple time points, and that
> the pathstats.byvoxel.txt files have different lengths between those two
> types of subjects.
> >
> > I suspect that the strange average path that you get has to do with
> how this mixing of subjects was done. Did you run the subjects with a
> single time point through the longitudinal stream as well?
> 
>  Yes, I ran the longitudinal stream for all subjects, also for the
> ones with only one time point.
> 
>  Thanks,
> 
>  Janosch
> 
> >
> > Best,
> > a.y
> >
> > On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote:
> >
> >> Hi Anastasia,
> >>
> >> yes, I am. But it looks similar in the distributed version :(
> >>
> >> Thanks,
> >>
> >> Janosch
> >>
> >>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu>:
> >>>
> >>>
> >>> Hi Janosch - Are you by any chance using the dev version of
> freeview?
> >>>
> >>> a.y
> >>>
> >>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote:
> >>>
>  Hi Anastasia and list,
> 
>  I'm trying to do analyses along the tract with the
> path_stats_byvoxel files.
> 
>  When I am visualizing the points using the waypoint functionality
> of Freeview, it looks a little strange, i.e., the points are not equally
> spaces on the tract, but clumped together at some parts and spread out on
> others, see:
> 
> 
> 
>  this looks different to your slides:
> 
> 
> 
>  Also, the 

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Ruopeng Wang]

Try 6.0.0beta.

On 11/03/2015 12:02 PM, Clara Kühn wrote:
> Our IT guy said it could be a software problem since he didn't have the 
> problem and the only difference between out computers was the display.
> We have these versions at the institute:
>
> 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
> Is the first one the dev version?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Ruopeng Wang" 
> An: "Freesurfer support list" 
> Gesendet: Dienstag, 3. November 2015 17:57:50
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> There was a bug in freeview in FS 5.3.0 that may have caused the crash. 
> Clara, can you try the dev version of freeview?
>
> Ruopeng
>
> On 11/03/2015 11:50 AM, Bruce Fischl wrote:
>
>
> Hi Clara
>
> that doesn't crash for me. Are you sure you ahve write permission to the 
> file? And that the disk isn't full? Ruopeng: any other ideas?
>
> Bruce
>
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Hi Bruce,
>
> I attached the wm.mgz from one of my participants. It happens with any 
> participant though.
> What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and 
> then it crashes with afore mentioned error message.
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Bruce Fischl" 
> An: "Freesurfer support list" 
> Gesendet: Dienstag, 3. November 2015 14:42:25
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> Hi Clara
>
> can you send us the wm.mgz and tell us exactly what you did to make it
> crash?
>
> thahks
> Bruce
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Dear FreeSurfer experts,
>
> since last week I have the problem that FS (5.3.0) crashes when I try to save 
> changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
> always restore it by renaming the temporary file (wm.mgz~) but it obviously 
> doen't save any changes.
>
> I've tried different computers (same FS version) and on some it works and on 
> some the same problem occurs. I just tried it on the 6.0.0beta version and it 
> saved like a charm. I would rather, however, keep editing my data with the 
> same version.
> Here is the error message I get in the terminal:
>
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal
>  [0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on 
> Apple to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
> 17:22:55 2015
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> Segmentation fault (core dumped)
>
> Any idea what it means by Segmentation Violation and how I can fix it??
> Cheers and thanks in advance!
> Clara Kühn
>
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>
> The information in this 

Re: [Freesurfer] changing the index of labels

[Douglas N Greve]

In that case you can do something like
fscalc lhfile.mgz add 1000 -o lhfile1000.mgz
mri_mask lhfile1000.mgz lhfile.mgz lhfile1000.mgz

This will add 1000 to the lhlabels. This will make the lh labels
different from the rh. You can add a constant to the rh too if you want.

doug


On 10/30/2015 07:12 PM, Jacobs H (NP) wrote:
> Yes, there are different mgz files for left and right (but they have the
> same index numbers and colors).
>
> On 10/30/15, 11:16 PM, "Douglas N Greve"  wrote:
>
>> Are there different files for the lh and rh? Sorry, never done the
>> subfields analysis.
>>
>>
>> On 10/30/2015 01:25 PM, Bruce Fischl wrote:
>>> Hi Heidi
>>>
>>> I guess you could do it yourself in matlab using the aseg to figure
>>> out which hemisphere you are in
>>>
>>> cheers
>>> Bruce
>>>
>>> On Fri, 30 Oct 2015, Jacobs H (NP) wrote:
>>>
 Hi,

 Is there a way to change the index of the segmentation of the
 hippocampal
 subfields, so that when I combine left and right, FreeSurfer treats
 them
 as different regions?

 Thanks!
 Best
 Heidi

>> I just checked again in freeview and indeed they have the same index
>> (e.g.
>> CA1 has value 206 for left and also for right).
>>
>> On 10/27/15, 5:01 PM, "Douglas Greve" 
>> wrote:
>>
>>> The color is not important. The question is whether they have a
>>> different index. Can you confirm that lh and rh have the same index?
>>>
>>> On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
 Hi Doug,

 Yes, for the aseg they are. But not for the hippocampal subfields:
 left
 and right have the same color coding.
 I am creating one segmentation, including left and right
 hippocampal
 subfields and aparc, for partial volume correction.
 Any idea how I can make the labels for the hippocampal subfields
 different
 (freesurfer version 6)?

 Thanks
 Heidi

 On 10/27/15, 4:32 PM, "Douglas Greve" 
 wrote:

> The indices should be different. Eg, 17 is left hippo, 53 is right
> hippo. If you click on them in freeview and different labels
> appear,
> then FS knows they are different
>
> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>> Hi.
>>
>> Just one another related question: now that I was able to combine
>> left
>> and
>> right hippocampal subfields with the aparc-aseg correctly, I
>> noticed
>> that
>> the left and right hippocampal subfields have the same color
>> labels
>> and
>> codes. What would be the best way to make sure that FreeSurfer
>> understand
>> that the left and right subfields (e.g. Left and right CA1) are
>> different
>> areas?
>>
>> Thanks!
>> Heidi
>>
>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>> 
>> wrote:
>>
>>> Thanks! Works wonderful!
>>> Heidi
>>>
>>> On 10/21/15, 10:50 PM, "Douglas N Greve"
>>> 
>>> wrote:
>>>
 If you want to remove them, you can use mri_binarize with the
 --replace
 option, replacing them with whatever you want.

 On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
> Hi,
>
> I am trying to generate a segmentation file containing the
> aseg+aparc
> but replacing the hippocampus with the hippocampal subfields.
> With mergeseg I was able to merge the segmentations, but
> unfortunately
> parts of the ³old² hippocampus (labeled as 17 and 53) are
> still
> in
> there (as the area covered by the subfields is not 100%
> equal to
> the
> hippocampus of the aseg).
> How can I remove the remains of the old hippocampal labels?
>
> Many thanks!
> Best
> Heidi
>
>
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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
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

Hi DOug,

doug.log is attached

the bash equivalent for |& is 2>&1 |

thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:


I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
sure what the bash equivalent is. Maybe |2 instead of |&
perhaps some bash experts can weigh in

On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:

Hi Doug,

Do you mean:

   mri_glmfit-sim --debug --glmdir 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?

When I tried running the same code with |& tee doug.log at the end, I kept 
getting:

syntax error near unexpected token `&'

Thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:


Can you run

mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
--cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log

and send me doug.log?




On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:

Hi experts,

I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.

My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I 
then ran mri_glmfit on the data.

I want to do my analysis/correction only in auditory cortex (AC) so I did my 
own simulation in AC of each hemisphere using mri_mcsim (as per 
http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).

So far, so good.

But when I try to run:

mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label 
AC --grf 4 neg --cwpvalthresh 0.05 --2space

I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
didn't help.

Any thoughts? Also, can you clarify which comparison neg vs pos will give me?

Thank you,

Susan McLaughlin, PhD
Research Scientist
Laboratory for Auditory Brain Sciences & Neuroengineering
Institute for Learning & Brain Sciences (I-LABS)
Portage Bay Bldg. Room 204
University of Washington, Box 357988
Seattle, WA 98195-7988

Ph: (206) 616-0102 Fx: (206) 221-6472
Cell: 206-850-8638
E-mail: s...@uw.edu


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

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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doug.log
Description: Binary data
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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[Martin Reuter]

Dear Pablo,
maybe what you want is a group x age interaction for each of those 
groups? (so 1x5 and 2x5)?
Not sure. It is your hypothesis, your model and we usually don't give 
advise on model building. Since you have a special case (within family 
analysis) I would recommend you try to get some advise from a 
bio-statistician, if unsure what you are doing.


Best, Martin


On 11/03/2015 12:01 PM, pablo najt wrote:

Dear Martin and FS experts.
I have a quick query about how to obtain my design matrix of /group by 
age/ from the following matlab command listed in the lme wiki. In the 
wiki example the matrix is created from variables 1 and 2 (group by time).


 X = [ones(length(M),1) M M(:,1).*M(:,2);

In my case I have a combination of variables 1 and 2 for group 
(relatives of PT and PT) and 5 (age).
I would really appreciate if you could kindly advice on how to adapt 
the command above to my design.

Thanks
Pablo


To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Tue, 27 Oct 2015 17:13:51 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within 
subject dataset {Disarmed}


Hi Pablo,

the sortData function sorts the rows so that entries from the same 
subject (in your case same family) are blocked and that within each 
block the time variable (2nd parameter specifies which column that is 
in your M matrix, in your case the first =1) is increasing.
It is important, when creating your design matrix X, that ordering 
agrees with Y. That is guaranteed if you generate X from M (which is 
ordered like Y after the sort command).


Best, Martin

On 10/27/2015 01:32 PM, pablo najt wrote:

Thank you for your input.
I noticed that if I follow literally all the steps in the wiki, my
data which is ordered by variable 'family' (instead of subjects,
in my case is number of members belonging to e.g. family_1) is
shuffled. This happens after I run the command sortData below.
Especially I noticed that ni and X do not match sID.
It would be really helpful to know what is this command doing. I
am wondering whether my data differs in number of columns or else
and because of this I end with a shuffled data. Any suggestion or
tips to figure what could be happening?
Thanks
Pablo

[M, Y, ni] = sortData(M,1,Y,sID)


To: freesurfer@nmr.mgh.harvard.edu

From: mreu...@nmr.mgh.harvard.edu 
Date: Wed, 14 Oct 2015 10:54:41 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within
subject dataset {Disarmed}

Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)

see
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

hope that helps, Martin


On 10/14/2015 10:43 AM, pablo najt wrote:

Dear FS experts.
I have query about a relating to a previous email (below). I
am aiming to run a LME analysis on cross-sectional data from
different families and have variable 'family' (number of
families) as my NI vector.
My design has three groups and therefore I am not able to use
qdec. I am running the matlab commands below and finding some
difficulty would really appreciate if you could help out.
Thanks
Pablo

Start analysis as follows:

1-Read your label eg.:
lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');

%-I input the concatenated .mgh image
from preproc and

mris_surf2surf---%

3-Fit a vertex-wise lme model with random effects.:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);

Here I am getting the following problems:

% If I use number of families as my ni
get the

following%

lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82,
lhcortex);

Error using lme_mass_fit (line 108)

The total number of measurements, indicated by
sum(ni), mustbe the same as the number of rows of
the design

matrix X

Error in lme_mass_fit_vw (line 73)

[stats1,st1] =
lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);

My matrix is organised in "family", "group", Sex" and

Re: [Freesurfer] FreeSurfer and OpenMP

[Julio Alberto González Torre]

One question about "-openmp". If I run multiple "recon-all" in different
terminals without using this flag...

Is there any problem with the 'gcareg' stage? For example, is there any
interference between subjects reconstruction?

Thanks.

2015-10-16 15:07 GMT+02:00 Bruce Fischl :

> Hi Linda
>
> did you actually include the angle brackets?  If so, try without them. And
> don't you want 4 there instead of 8 (if you have 4 processors)?
>
> On
> Fri, 16 Oct 2015, Linda BOUMGHAR wrote:
>
> > I would like to use freesurfer with OpenMP, with 4 processors. I wrote
> this :
> > recon-all -all -i
> > /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid
> > subj1 -openmp <8>
> > and I got this error message :
> >
> > bash: syntax error near unexpected token `8'
> >
> > What is the good syntax if I want tu use OpenMP, please?
> > Great regards,
> > Linda Boumghar
> >
> > 
> > This message was sent using IMP, the Internet Messaging Program.
> >
> >
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> >
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

Can you run

mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
--cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log

and send me doug.log?




On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
> Hi experts,
>
> I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
>
> My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. 
> I then ran mri_glmfit on the data.
>
> I want to do my analysis/correction only in auditory cortex (AC) so I did my 
> own simulation in AC of each hemisphere using mri_mcsim (as per 
> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>
> So far, so good.
>
> But when I try to run:
>
> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>
> I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
> didn't help.
>
> Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
>
> Thank you,
>
> Susan McLaughlin, PhD
> Research Scientist
> Laboratory for Auditory Brain Sciences & Neuroengineering
> Institute for Learning & Brain Sciences (I-LABS)
> Portage Bay Bldg. Room 204
> University of Washington, Box 357988
> Seattle, WA 98195-7988
>
> Ph: (206) 616-0102 Fx: (206) 221-6472
> Cell: 206-850-8638
> E-mail: s...@uw.edu
>
>
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MGH-NMR Center
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Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] reproducing sig.mgh

[Douglas N Greve]

Look in the output folder for a file called Xg.dat. This is the design 
matrix used by QDEC. Compare that to the design matrix from your ANOVA

On 10/28/2015 11:13 PM, Eric Cunningham wrote:
> Hello Freesurfer Experts,
>
> I am trying to reproduce the values in sig.mgh using matlab, just to 
> confirm that I know what is going on.  My numbers do not match 
> exactly, and I am hoping someone can explain my error, or point me in 
> the right direction.
>
> With Qdec, I built a model with one discrete factor (A) with groups 
> (A1) and (A2), one continuous covariate (B), and one nuisance factor 
> (C).  I extracted the values from sig.mgh from the folder: 
> lh-Diff-A1-A2-Cor-area-B at a specific vertex.  I also extracted the 
> values from y.mgh at the same vertex.  I then ran an anova with 
> contrast matrix, and expected the -log10(p-value) of the A*B term to 
> match that of sig.mgh.
> [1 0 0;...   (A)
> 0 1 0;...(B)
> 0 0 1;...(C)
> 1 1 0];  (A*B)
>
> Thank you for your time,
> -E
>
>
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

I meant &. The & works for tcsh (or csh). Are you using bash? I'm not 
sure what the bash equivalent is. Maybe |2 instead of |&
perhaps some bash experts can weigh in

On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
> Do you mean:
>
>mri_glmfit-sim --debug --glmdir 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>  --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
>
> When I tried running the same code with |& tee doug.log at the end, I kept 
> getting:
>
> syntax error near unexpected token `&'
>
> Thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> Can you run
>>
>> mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
>>
>> and send me doug.log?
>>
>>
>>
>>
>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>>> Hi experts,
>>>
>>> I am having trouble performing a Monte Carlo correction using 
>>> mri_glmfit-sim.
>>>
>>> My data were sampled to fsaverage and smoothed at fwhm 5, using 
>>> mris_preproc. I then ran mri_glmfit on the data.
>>>
>>> I want to do my analysis/correction only in auditory cortex (AC) so I did 
>>> my own simulation in AC of each hemisphere using mri_mcsim (as per 
>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>>
>>> So far, so good.
>>>
>>> But when I try to run:
>>>
>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>>
>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
>>> didn't help.
>>>
>>> Any thoughts? Also, can you clarify which comparison neg vs pos will give 
>>> me?
>>>
>>> Thank you,
>>>
>>> Susan McLaughlin, PhD
>>> Research Scientist
>>> Laboratory for Auditory Brain Sciences & Neuroengineering
>>> Institute for Learning & Brain Sciences (I-LABS)
>>> Portage Bay Bldg. Room 204
>>> University of Washington, Box 357988
>>> Seattle, WA 98195-7988
>>>
>>> Ph: (206) 616-0102 Fx: (206) 221-6472
>>> Cell: 206-850-8638
>>> E-mail: s...@uw.edu
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>>
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>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

it cannot find this file

/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat

which should have been created by mri_glmfit. What is your mri_glmfit 
command line?

Also, don't use --grf, that is for volumes only


On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
> Hi DOug,
>
> doug.log is attached
>
> the bash equivalent for |& is 2>&1 |
>
> thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
>> sure what the bash equivalent is. Maybe |2 instead of |&
>> perhaps some bash experts can weigh in
>>
>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
>>> Hi Doug,
>>>
>>> Do you mean:
>>>
>>>mri_glmfit-sim --debug --glmdir 
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>>>  
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee 
>>> doug.log?
>>>
>>> When I tried running the same code with |& tee doug.log at the end, 
>>> I kept getting:
>>>
>>> syntax error near unexpected token `&'
>>>
>>> Thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 Can you run

 mri_glmfit-sim --debug --glmdir [my data 
 dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg 
 --cwpvalthresh 0.05 --2space |& tee doug.log

 and send me doug.log?




 On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
> Hi experts,
>
> I am having trouble performing a Monte Carlo correction using 
> mri_glmfit-sim.
>
> My data were sampled to fsaverage and smoothed at fwhm 5, using 
> mris_preproc. I then ran mri_glmfit on the data.
>
> I want to do my analysis/correction only in auditory cortex (AC) 
> so I did my own simulation in AC of each hemisphere using 
> mri_mcsim (as per 
> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>
> So far, so good.
>
> But when I try to run:
>
> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>
> I get "fwhm: Undefined variable." I tried adding --fwhm-override 
> 5, but it didn't help.
>
> Any thoughts? Also, can you clarify which comparison neg vs pos 
> will give me?
>
> Thank you,
>
> Susan McLaughlin, PhD
> Research Scientist
> Laboratory for Auditory Brain Sciences & Neuroengineering
> Institute for Learning & Brain Sciences (I-LABS)
> Portage Bay Bldg. Room 204
> University of Washington, Box 357988
> Seattle, WA 98195-7988
>
> Ph: (206) 616-0102 Fx: (206) 221-6472
> Cell: 206-850-8638
> E-mail: s...@uw.edu
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

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

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


>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>>
>
>
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

Hi Doug,

Do you mean:

  mri_glmfit-sim --debug --glmdir 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?

When I tried running the same code with |& tee doug.log at the end, I kept 
getting:

syntax error near unexpected token `&'

Thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

>
> Can you run
>
> mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
>
> and send me doug.log?
>
>
>
>
> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>> Hi experts,
>>
>> I am having trouble performing a Monte Carlo correction using mri_glmfit-sim.
>>
>> My data were sampled to fsaverage and smoothed at fwhm 5, using 
>> mris_preproc. I then ran mri_glmfit on the data.
>>
>> I want to do my analysis/correction only in auditory cortex (AC) so I did my 
>> own simulation in AC of each hemisphere using mri_mcsim (as per 
>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>
>> So far, so good.
>>
>> But when I try to run:
>>
>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>
>> I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
>> didn't help.
>>
>> Any thoughts? Also, can you clarify which comparison neg vs pos will give me?
>>
>> Thank you,
>>
>> Susan McLaughlin, PhD
>> Research Scientist
>> Laboratory for Auditory Brain Sciences & Neuroengineering
>> Institute for Learning & Brain Sciences (I-LABS)
>> Portage Bay Bldg. Room 204
>> University of Washington, Box 357988
>> Seattle, WA 98195-7988
>>
>> Ph: (206) 616-0102 Fx: (206) 221-6472
>> Cell: 206-850-8638
>> E-mail: s...@uw.edu
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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] Monte Carlo in mri_glmfit-sim

[smcl]

I am using bash. I am trying to google the bash equivalent of tcsh |&, but if 
anybody knows it, please let me know.

thanks,
Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
> sure what the bash equivalent is. Maybe |2 instead of |&
> perhaps some bash experts can weigh in
>
> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
>> Hi Doug,
>>
>> Do you mean:
>>
>>mri_glmfit-sim --debug --glmdir 
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>>  --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log?
>>
>> When I tried running the same code with |& tee doug.log at the end, I kept 
>> getting:
>>
>> syntax error near unexpected token `&'
>>
>> Thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> Can you run
>>>
>>> mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log
>>>
>>> and send me doug.log?
>>>
>>>
>>>
>>>
>>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
 Hi experts,

 I am having trouble performing a Monte Carlo correction using 
 mri_glmfit-sim.

 My data were sampled to fsaverage and smoothed at fwhm 5, using 
 mris_preproc. I then ran mri_glmfit on the data.

 I want to do my analysis/correction only in auditory cortex (AC) so I did 
 my own simulation in AC of each hemisphere using mri_mcsim (as per 
 http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).

 So far, so good.

 But when I try to run:

 mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm 
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space

 I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it 
 didn't help.

 Any thoughts? Also, can you clarify which comparison neg vs pos will give 
 me?

 Thank you,

 Susan McLaughlin, PhD
 Research Scientist
 Laboratory for Auditory Brain Sciences & Neuroengineering
 Institute for Learning & Brain Sciences (I-LABS)
 Portage Bay Bldg. Room 204
 University of Washington, Box 357988
 Seattle, WA 98195-7988

 Ph: (206) 616-0102 Fx: (206) 221-6472
 Cell: 206-850-8638
 E-mail: s...@uw.edu


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> 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.
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

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Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

[Douglas N Greve]

The y.mgh file is created by your call to mris_preproc (or by a 
subsequent call to mri_surf2surf for smoothing). The order of the 
subjects depends on how you called mris_preproc (which should match that 
in the fsgd file or else everything will be bogus). The y.mgh file 
contains all the subjects in fsaverage space, so you don't need to run 
it for each subject or resample back into native space

On 11/03/2015 02:29 PM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> Thanks for the reply. Sure I will try this command. But as it is now, how 
> will mri_segstats know the order in the fsgd file? Also, this command needs 
> to run for each subject, right? Then, which input file should I use for the 
> --i flag?
>
> mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh--id 1 
> --avgwf y.label.dat
>
>
> Thanks a lot!
> Hamdi
>
> 
> 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: Tuesday, November 03, 2015 2:01 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a 
> ROI
>
> On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
>> Sorry, the figures I inserted in the text did not appear in the email.
>> I attach them now.
>>
>> Best,
>> Hamdi
>>
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H.
>> Hamdi [hamdi.eryil...@mgh.harvard.edu]
>> *Sent:* Friday, October 30, 2015 1:32 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] cortical thickness - comparing two groups
>> within a ROI
>>
>> Dear FS experts,
>>
>> I have a question about extracting average cortical thickness from a
>> manually created ROI. I am comparing 2 groups, namely PostFort and
>> PreFort and my fsgd file appears as the following:
>>
>> GroupDescriptorFile 1
>> Title PostPreFortification
>> Class PostFort
>> Class PreFort
>>
>> InputSubject1PostFort
>> InputSubject2PostFort
>> .
>> .
>> .
>>
>> The contrast that I use to compare these groups is [1 -1]. When I
>> display the significance map for this contrast I get the following
>> image on the left hemisphere:
>>
>>
>>
>>
>> My first question is, those blue clusters represent regions, where
>> thickness is greater in the PreFort group, don't they?
> Correct
>> Assuming this is correct, I created a label for this region (which
>> contains about 3000 vertices) and extracted the thickness value from
>> this region for each subject using the following commands. These
>> commands are part of scripts in which $subject and $label are defined.
>>
>>
>>
>> _to make a label for each subject (the original label was created on
>> fsaverage):_
>> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label
>> --srcsubject fsaverage --trglabel
>> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
>> --regmethod surface --hemi lh
>>
>> _to create a stats file of this ROI containing several anatomical
>> measures:_
>> *mris_anatomical_stats* -f
>> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
>> $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
>>
>> _to compile thickness values from all subjects into one table: _
>> *aparcstats2table* --hemi lh --subjectsfile
>> $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc
>> NP_PostMINUSPre_IPS.label --meas thickness --tablefile
>> $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt
>>
>> This table displays the average thickness value of my ROI for each
>> subject. Based on this table I calculated the mean thickness for each
>> group, which is as the following:
>>
>> PostFort: 3.043
>> PreFort: 2.842
>>
>> My question is: If this cluster appears blue in the Post>Pre map,
>> shouldn't the thickness have been greater in the PreFort group? Or am
>> I missing a step?
> Not sure. The commands look right. Can you try something else?
> mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh
> --id 1 --avgwf y.label.dat
>
> This should create a single column of numbers in y.label.dat that
> correspond to the mean thickness in the label of each  subject as
> ordered in your fsgd file. See if you get similar numbers to your method
> doug
>
>
>
>> Many thanks in advance!
>>
>> Best,
>> Hamdi
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>> Freesurfer mailing list
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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
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> 

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

[Douglas N Greve]

On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
> Sorry, the figures I inserted in the text did not appear in the email. 
> I attach them now.
>
> Best,
> Hamdi
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H. 
> Hamdi [hamdi.eryil...@mgh.harvard.edu]
> *Sent:* Friday, October 30, 2015 1:32 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] cortical thickness - comparing two groups 
> within a ROI
>
> Dear FS experts,
>
> I have a question about extracting average cortical thickness from a 
> manually created ROI. I am comparing 2 groups, namely PostFort and 
> PreFort and my fsgd file appears as the following:
>
> GroupDescriptorFile 1
> Title PostPreFortification
> Class PostFort
> Class PreFort
>
> InputSubject1PostFort
> InputSubject2PostFort
> .
> .
> .
>
> The contrast that I use to compare these groups is [1 -1]. When I 
> display the significance map for this contrast I get the following 
> image on the left hemisphere:
>
>
>
>
> My first question is, those blue clusters represent regions, where 
> thickness is greater in the PreFort group, don't they?
Correct
> Assuming this is correct, I created a label for this region (which 
> contains about 3000 vertices) and extracted the thickness value from 
> this region for each subject using the following commands. These 
> commands are part of scripts in which $subject and $label are defined.
>
>
>
> _to make a label for each subject (the original label was created on 
> fsaverage):_
> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label 
> --srcsubject fsaverage --trglabel 
> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject 
> --regmethod surface --hemi lh
>
> _to create a stats file of this ROI containing several anatomical 
> measures:_
> *mris_anatomical_stats* -f 
> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l 
> $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
>
> _to compile thickness values from all subjects into one table: _
> *aparcstats2table* --hemi lh --subjectsfile 
> $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc 
> NP_PostMINUSPre_IPS.label --meas thickness --tablefile 
> $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt
>
> This table displays the average thickness value of my ROI for each 
> subject. Based on this table I calculated the mean thickness for each 
> group, which is as the following:
>
> PostFort: 3.043
> PreFort: 2.842
>
> My question is: If this cluster appears blue in the Post>Pre map, 
> shouldn't the thickness have been greater in the PreFort group? Or am 
> I missing a step?
Not sure. The commands look right. Can you try something else?
mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh 
--id 1 --avgwf y.label.dat

This should create a single column of numbers in y.label.dat that 
correspond to the mean thickness in the label of each  subject as 
ordered in your fsgd file. See if you get similar numbers to your method
doug



>
> Many thanks in advance!
>
> Best,
> Hamdi
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Ruopeng Wang]

There was a bug in freeview in FS 5.3.0 that may have caused the crash. 
Clara, can you try the dev version of freeview?


Ruopeng

On 11/03/2015 11:50 AM, Bruce Fischl wrote:

Hi Clara

that doesn't crash for me. Are you sure you ahve write permission to 
the file? And that the disk isn't full? Ruopeng: any other ideas?


Bruce

On Tue, 3 Nov 2015, Clara Kühn wrote:


Hi Bruce,

I attached the wm.mgz from one of my participants. It happens with 
any participant though.
What I did is add wm voxels ( 147, 106, 68 ) and klick the save 
button and then it crashes with afore mentioned error message.


Cheers, Clara

- Ursprüngliche Mail -
Von: "Bruce Fischl" 
An: "Freesurfer support list" 
Gesendet: Dienstag, 3. November 2015 14:42:25
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Hi Clara

can you send us the wm.mgz and tell us exactly what you did to make it
crash?

thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:


Dear FreeSurfer experts,

since last week I have the problem that FS (5.3.0) crashes when I 
try to save changes to the wm.mgz. It closes immediately and the 
wm.mgz is deleted. I can always restore it by renaming the temporary 
file (wm.mgz~) but it obviously doen't save any changes.


I've tried different computers (same FS version) and on some it 
works and on some the same problem occurs. I just tried it on the 
6.0.0beta version and it saved like a charm. I would rather, 
however, keep editing my data with the same version.

Here is the error message I get in the terminal:

[0]PETSC ERROR: 
 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation 
Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or 
-on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC 
ERROR: or try http://valgrind.org on linux or man libgmalloc on 
Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, 
link, and run

[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 


[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 
 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 
17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 
 

[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn 
Fri Oct 30 17:22:55 2015
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt

[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 
--with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 
COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 
 

[0]PETSC ERROR: User provided function() line 0 in unknown directory 
unknown file

[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn

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Re: [Freesurfer] First-level analysis (native vs fsaverage)

[Douglas N Greve]

In the native space analysis the data get smoothed in the 3d volume and 
then projecting to the surface. This is very different from a 
surface-based analysis where you project to the surface and then smooth 
in 2D. For one thing, 5mm FWHM in one analysis is not the same as 5mm 
FWHM in the other. You get much more smoothing in the volume at 5mm than 
you do on the surface. Why one is better than the other is hard to say. 
You might try cranking up the smoothing for the surface-based analysis.

doug


On 11/02/2015 04:29 PM, Rodriguez-Thompson, Anais wrote:
> Hi freesurfer experts,
>
> I have a question about how running first-level analyses in either native 
> space or fsaverage space changes activation. My original analysis was a 
> per-session analysis run on native space.  The command used to make the 
> analysis was
>
> ANALYSIS 1:
> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm 
> slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -native 
> -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 
> 2
>
> However, my lab was interested in running our analyses -per-run, so I created 
> a new per-run analysis on the fsaverage brain using the command:
>
> ANALYSIS 2:
> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915_lh -TR 2 
> -paradigm slopepar -event-related -runlistfile runlistfile -tpef 
> tpef_1.5mm.txt -surface fsaverage lh -fwhm 5 -per-run -timewindow 20 -TER 2 
> -nconditions 9 -gammafit 2.25 1.25 -refevendur 2 -fsd bold
>
> The group maps for the two looked comparable. However, I covaried those maps 
> with performance on our task. The maps looked significantly different, and 
> while 9 cluster survived MC correction from analysis 1 (3 LH, 6 RH), only 3 
> survived MC correction from analysis 2 (0 LH, 2 RH).
>
> I thought that the difference could have been due to per-run vs. per-session 
> MC, but I created a test analysis (per-session, fsaverage space), and this 
> analysis looked more like the 2nd analysis than the 1st, leading me to 
> believe that the difference in activation was due to running the first-level 
> analysis on fsaverage space rather than native space.
>
> The command I used for the test analysis was: mkanalysis-sess -analysis 
> TEST_fsaverage_persession_lh -TR 2 -paradigm slopepar -surface fsaverage lh 
> -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
> -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 
> 5 -per-session
>
> Do you know why running first-level analyses on fsaverage space rather than 
> native space would decrease activation effects, leading to fewer significant 
> clusters after MC correction?
>
> I've attached a pdf file with the maps in question.
>
> Thanks,
> Anais
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] First-level analysis (native vs fsaverage)

[Rodriguez-Thompson, Anais]

Thanks for your response. In general, is it better practice to run the first 
level analysis in the native space, and then resample the subjects to fsaverage 
space during concatenation, or to resample the subjects to fsaverage space 
during first level analysis?

Best,
Anais

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: Tuesday, November 03, 2015 12:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] First-level analysis (native vs fsaverage)

In the native space analysis the data get smoothed in the 3d volume and
then projecting to the surface. This is very different from a
surface-based analysis where you project to the surface and then smooth
in 2D. For one thing, 5mm FWHM in one analysis is not the same as 5mm
FWHM in the other. You get much more smoothing in the volume at 5mm than
you do on the surface. Why one is better than the other is hard to say.
You might try cranking up the smoothing for the surface-based analysis.

doug


On 11/02/2015 04:29 PM, Rodriguez-Thompson, Anais wrote:
> Hi freesurfer experts,
>
> I have a question about how running first-level analyses in either native 
> space or fsaverage space changes activation. My original analysis was a 
> per-session analysis run on native space.  The command used to make the 
> analysis was
>
> ANALYSIS 1:
> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm 
> slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -native 
> -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 
> 2
>
> However, my lab was interested in running our analyses -per-run, so I created 
> a new per-run analysis on the fsaverage brain using the command:
>
> ANALYSIS 2:
> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915_lh -TR 2 
> -paradigm slopepar -event-related -runlistfile runlistfile -tpef 
> tpef_1.5mm.txt -surface fsaverage lh -fwhm 5 -per-run -timewindow 20 -TER 2 
> -nconditions 9 -gammafit 2.25 1.25 -refevendur 2 -fsd bold
>
> The group maps for the two looked comparable. However, I covaried those maps 
> with performance on our task. The maps looked significantly different, and 
> while 9 cluster survived MC correction from analysis 1 (3 LH, 6 RH), only 3 
> survived MC correction from analysis 2 (0 LH, 2 RH).
>
> I thought that the difference could have been due to per-run vs. per-session 
> MC, but I created a test analysis (per-session, fsaverage space), and this 
> analysis looked more like the 2nd analysis than the 1st, leading me to 
> believe that the difference in activation was due to running the first-level 
> analysis on fsaverage space rather than native space.
>
> The command I used for the test analysis was: mkanalysis-sess -analysis 
> TEST_fsaverage_persession_lh -TR 2 -paradigm slopepar -surface fsaverage lh 
> -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
> -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 
> 5 -per-session
>
> Do you know why running first-level analyses on fsaverage space rather than 
> native space would decrease activation effects, leading to fewer significant 
> clusters after MC correction?
>
> I've attached a pdf file with the maps in question.
>
> Thanks,
> Anais
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Voxel based vs surface based

[Douglas N Greve]

I think the thing with VBM is that it is hard to get your head around 
what is actually being measured. The quantity is called "gray matter 
density" which is a number between 0 (no GM) and 1 (full GM). This is 
used in two overlapping contexts. At the voxel level, the density is 
determined by the voxel intensity. Eg, if GM in the atlas is typically 
100 and WM is 80 and the voxel is 90, then it may get a density of 0.5. 
This can happen because the voxel is on the boundary between full GM and 
full WM (ie, a partial volume effect) or it may be that it is in a 
structure that has a large mixture of GM and WM. Eg, pallidum will have 
a GM density much less than 1. The second context appears when you 
smooth the data. This replaces the voxel-wise GM density with an average 
in a given neighborhood. This also gives a number between 0 and 1 and 
can more-or-less be thought of as the amount of GM in the sphere of the 
smoothing kernel. For example, when someone is young, they have a nice 
plump cortex where the gyri nearly press into each other (small sulcal 
spaces). As one gets older, the brain loses tissue in a complicated 
spatial pattern. Some of it GM, some of it WM. As the brain atrophies, 
it starts to unfold a bit, meaning that the sulcal spaces get larger. 
This may be due to loss of GM or WM near that sulcus or loss of tissue 
remotely. In either case, the GM density in this area will drop 
regardless of whether there is actual loss of GM there or not. This 
makes VBM hard to interpret.

With surface-based thickness analysis, we are only looking at GM and the 
effect can only be local. Furthermore, the intersubject registration is 
driven by the folding patterns of the white surface. These are 
independent of the thickness measurement. In VBM, the intersubject 
registration is driven by the GM density itself, meaning that the metric 
is confounded by the fit to the atlas. This further complicates the 
interpretation. I don't mean to say that VBM analysis is not useful, 
just that it is hard to interpret and that differences with 
surface-based analysis should not come as a surprise.

doug



On 10/30/2015 01:09 PM, O'Shea,Andrew wrote:
> Hello John,
> I would highly recommend you take a look at this paper 
> http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf 
> (Greve, 
> 2011. An Absolute Beginner’s Guide to Surface- and Voxel-
> based Morphometric Analysis). I have found it to be very helpful for 
> my understanding.
> -Andrew
>
> From:  > on behalf of John 
> Anderson >
> Reply-To: "freesurfer@nmr.mgh.harvard.edu 
> " 
> >
> Date: Friday, October 30, 2015 at 10:54 AM
> To: "freesurfer@nmr.mgh.harvard.edu 
> " 
> >
> Subject: [Freesurfer] Voxel based vs surface based
>
> Hi Doug and Bruce,
> Kindly, I have question regarding the difference between voxel based ( 
> VBM/ FSL pipeline) and surface based analysis ( Freesurfer ).
>
> I have two groups of subjects Group A and Group B
> I ran morphometric analysis in Freesurfer ( recon-all then manual 
> edits) to check the difference in cortical thickness between the 
> groups. Then I used Qdec to correct the results for multiple 
> comparisons and to visualize the significant clusters.
> Then I ran VBM analysis between the groups ( the same subjects) to 
> study the difference in gray matter volume between the groups.
>
> I got significant difference between the groups in both methods but in 
> different areas of the brain ( the significant clusters are not in the 
> same location ).
>
> What is the difference between surface based analysis and voxel based 
> analysis technically. Is it right to get different results?
>
> Thanks in advance
> Bests,
> John
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Extracing values from ces.nii

[Douglas N Greve]

It should be interpreted as a 2D structure of size 27307*6= 163842 
which are the number of vertices in fsaverage


On 10/29/2015 11:41 AM, Afzal, Afsana wrote:
> Hi,
>
> I'm trying to extract the contrast values from ces.nii.gz after 
> first-level analysis. My goal is to average the contrast values for 
> each voxel across subjects for a given condition and see where an 
> individual from a separate population falls within the distribution of 
> contrast values.
>
> The ces.nii file I'm working with has the following dimension: (27307, 
> 1, 6, 1), which I interpreted as containing information about 27307 
> voxels in a 3D matrix. What does the information in the 6 rows for 
> each voxel represent? I was expecting to get a single raw b-value for 
> each voxel. The structure is consistent with sig.nii and t.nii files 
> as well.
>
> Thanks for any help,
>
> Afsana
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] R: Re: error vcsf.config

[Douglas N Greve]

If there are no CSF voxels in the native functional space, there are a 
couple of things to do. (1) don't use a CSF regressor for any of  your 
subjects, or (2) change the fill threshold for all subjects. The default 
is .95, meaning a voxel has to be at least 95% CSF for it to be 
classified as CSF in the seed.

doug

On 10/30/2015 02:42 PM, std...@virgilio.it wrote:
> Yes, the ventricle is very small.
> The segmentation in aparc and aseg is nice.
> How can I do to analyze this subject? I need to include it in the 
> analysis.
> Many thanks,
>
>
> Stefano
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 30-ott-2015 16.03
> A: 
> Ogg: Re: [Freesurfer] error vcsf.config
>
> That means it could not find any CSF voxels. Try checking the
> registration. It could also be that this is a subject with really
> small ventricles.
>
> On 10/30/15 3:57 AM, std...@virgilio.it wrote:
>>
>> Hi list,
>>
>>
>> During fcseed-sess -s subj -cfg vcsf.config
>>
>>
>> a subject produces the follow error.
>>
>> I have rerun recon-all, cheched aparc+aseg with tkmedit. They
>> seem to be ok.
>>
>> Why this error is produced?
>>
>>
>> Thanks
>>
>>
>>
>> Stefano
>>
>>
>>
>> Creating output directory
>> 
>> /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm
>>
>> Loading y from
>> /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz
>>
>> Saving design matrix to
>> 
>> /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat
>>
>> Normalized matrix condition is 61.5872
>>
>> Matrix condition is 1e+08
>>
>> Pruning voxels by thr: 0.00
>>
>> Found 0 voxels in mask
>>
>> Saving mask to
>> 
>> /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh
>>
>> search space = 0.00
>>
>> DOF = 297
>>
>> Starting fit and test
>>
>> Fit completed in 0.0008 minutes
>>
>> Computing temporal AR1
>>
>> Writing results
>>
>> Computing FSNR
>>
>>   mean
>>
>> maxvox sig=0  F=0  at  index 0 0 0seed=1446518089
>>
>>   linear
>>
>> maxvox sig=0  F=0  at  index 0 0 0seed=1446518089
>>
>>   quad
>>
>> maxvox sig=0  F=0  at  index 0 0 0seed=1446518089
>>
>> Computing PCA (300)
>>
>> ERROR: no voxels in mask
>>
>>
>>
>> ___
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>
>
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] R: Re: average z-score of each subject from a common cluster

[Douglas N Greve]

look in the summaryfile. Also, don't use --seg z.nii.gz. In the command 
below, it works because you have --annot afterwards, but in general it 
is not correct

On 10/30/2015 04:22 PM, std...@virgilio.it wrote:
> Thanks.
> I have obtained:
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>
> cwd
>
> cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc --i 
> z.nii.gz --sum summaryfile
>
> sysname  Darwin
>
> hostname iMac-di-Stefano.local
>
> machine  x86_64
>
> user Stefano
>
> UseRobust  0
>
> Loading z.nii.gz
>
> Loading z.nii.gz
>
> Voxel Volume is 1 mm^3
>
> Generating list of segmentation ids
>
> Found  22 segmentations
>
> Computing statistics for each segmentation
>
>   0-7   2   2.000
>
>   1-6 110 110.000
>
>   2-5 255 255.000
>
>   3-4 518 518.000
>
>   4-3   11901190.000
>
>   5-2   16921692.000
>
>   6-1   41044104.000
>
>   7 0   61577   61577.000
>
>   8 1   42598   42598.000
>
>   9 2   28146   28146.000
>
>  10 3   14859   14859.000
>
>  11 4   58455845.000
>
>  12 5   18991899.000
>
>  13 6 485 485.000
>
>  14 7 116 116.000
>
>  15 8 75  75.000
>
>  16 9 74  74.000
>
>  1710 78  78.000
>
>  1811 65  65.000
>
>  1912 104 104.000
>
>  2013 45  45.000
>
>  2114   5   5.000
>
>
> How I can know the meaning of this number? Where is z?
>
> I have tried also with:
>
> mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii.gz 
> --sum summaryfile --mask 
> .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13.neg.sig.masked.nii.gz
>  
> --avgwfvol mrivol
>
>
> but I have problem with interpretation.
>
>
>
> Stefano
>
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 30-ott-2015 16.17
> A: 
> Ogg: Re: [Freesurfer] average z-score of each subject from a
> common cluster
>
>
>
> On 10/30/15 7:16 AM, std...@virgilio.it wrote:
>> Hi list,
>> I have two queries, please.
>>
>> I'd like to have the z-score from my rsfMRI data (seed-analyis).
>>
>> 1) I have extract the z-score from the Vtx Max
>>
>> In details, after groups comparison analysis, I have opened
>> the cache.th13.pos.sig.cluster.summary contained in group.diff
>> folder and I have read the Vtx Max coordinates.
>> Next, I have open the z.nii.gz of each subject and I have
>> expected the z-score from the vertex which have the Vtx Max
>> coordinates.
>>
>> Is this procedure corrected?
> Yes
>>
>> 2) z-score of each subject from a common cluster
>>
>> I would like to use the cluster which shows the group difference
>> (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would
>> extract from it the average of the z-score which is contained in
>> each subject.
>> How should I do?
> Use mri_segstats passing the z map as the input (--i) and the
> cluster map as the seg. The output will be --sum. Run with --help
> for more info
>>
>> Thanks.
>>
>>
>> Stefano
>>
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] zcat issue, lGI processing

[Douglas N Greve]

you can find out where it is with
   which zcat

On 11/03/2015 07:42 AM, Andrews, Derek wrote:
> Hello Freesurfer Support Team,
>
> I have encountered an issue running recon-all –lgi that I believe is 
> due to a zcat issue on mac OSx where a .Z is added to the end of the 
> file name the resulting error looks like this…
>
> >> reading filled volume...
>
> zcat: can't stat: 
> /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
>  
> (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z):
>  
> No such file or directory
>
>
> Upon reading through some message boards it appears replacing zcat 
> with gzcat can solve this issue, however I am unsure where this 
> troublesome zcat command is (it does not appear in the mriscomputelgi 
> script).
>
>
> Any suggestions or work throughs would be appreciated.
>
>
> Best, Derek
>
>
>
> 
>
> *Derek Sayre Andrews, MSc*
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
>
> Department of Forensic and Neurodevelopmental Sciences
>
> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
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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
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Re: [Freesurfer] First-level analysis (native vs fsaverage)

[Rodriguez-Thompson, Anais]

Great, thank you. In terms of smoothing, I don't want to arbitrarily increase 
smoothing to find effects. Is there an optimal amount of smoothing that should 
be performed on the surface?

Thanks,
Anais

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: Tuesday, November 03, 2015 1:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] First-level analysis (native vs fsaverage)

Resample to the surface and then smooth is better.

On 11/03/2015 01:12 PM, Rodriguez-Thompson, Anais wrote:
> Thanks for your response. In general, is it better practice to run the first 
> level analysis in the native space, and then resample the subjects to 
> fsaverage space during concatenation, or to resample the subjects to 
> fsaverage space during first level analysis?
>
> Best,
> Anais
> 
> 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: Tuesday, November 03, 2015 12:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] First-level analysis (native vs fsaverage)
>
> In the native space analysis the data get smoothed in the 3d volume and
> then projecting to the surface. This is very different from a
> surface-based analysis where you project to the surface and then smooth
> in 2D. For one thing, 5mm FWHM in one analysis is not the same as 5mm
> FWHM in the other. You get much more smoothing in the volume at 5mm than
> you do on the surface. Why one is better than the other is hard to say.
> You might try cranking up the smoothing for the surface-based analysis.
>
> doug
>
>
> On 11/02/2015 04:29 PM, Rodriguez-Thompson, Anais wrote:
>> Hi freesurfer experts,
>>
>> I have a question about how running first-level analyses in either native 
>> space or fsaverage space changes activation. My original analysis was a 
>> per-session analysis run on native space.  The command used to make the 
>> analysis was
>>
>> ANALYSIS 1:
>> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm 
>> slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt 
>> -native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 
>> -refeventdur 2
>>
>> However, my lab was interested in running our analyses -per-run, so I 
>> created a new per-run analysis on the fsaverage brain using the command:
>>
>> ANALYSIS 2:
>> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915_lh -TR 2 
>> -paradigm slopepar -event-related -runlistfile runlistfile -tpef 
>> tpef_1.5mm.txt -surface fsaverage lh -fwhm 5 -per-run -timewindow 20 -TER 2 
>> -nconditions 9 -gammafit 2.25 1.25 -refevendur 2 -fsd bold
>>
>> The group maps for the two looked comparable. However, I covaried those maps 
>> with performance on our task. The maps looked significantly different, and 
>> while 9 cluster survived MC correction from analysis 1 (3 LH, 6 RH), only 3 
>> survived MC correction from analysis 2 (0 LH, 2 RH).
>>
>> I thought that the difference could have been due to per-run vs. per-session 
>> MC, but I created a test analysis (per-session, fsaverage space), and this 
>> analysis looked more like the 2nd analysis than the 1st, leading me to 
>> believe that the difference in activation was due to running the first-level 
>> analysis on fsaverage space rather than native space.
>>
>> The command I used for the test analysis was: mkanalysis-sess -analysis 
>> TEST_fsaverage_persession_lh -TR 2 -paradigm slopepar -surface fsaverage lh 
>> -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
>> -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 
>> -fwhm 5 -per-session
>>
>> Do you know why running first-level analyses on fsaverage space rather than 
>> native space would decrease activation effects, leading to fewer significant 
>> clusters after MC correction?
>>
>> I've attached a pdf file with the maps in question.
>>
>> Thanks,
>> Anais
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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>
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> 

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

[Eryilmaz, H. Hamdi]

Hi Doug, 

Thanks for the reply. Sure I will try this command. But as it is now, how will 
mri_segstats know the order in the fsgd file? Also, this command needs to run 
for each subject, right? Then, which input file should I use for the --i flag? 

mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh--id 1 
--avgwf y.label.dat


Thanks a lot!
Hamdi


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: Tuesday, November 03, 2015 2:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
> Sorry, the figures I inserted in the text did not appear in the email.
> I attach them now.
>
> Best,
> Hamdi
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H.
> Hamdi [hamdi.eryil...@mgh.harvard.edu]
> *Sent:* Friday, October 30, 2015 1:32 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] cortical thickness - comparing two groups
> within a ROI
>
> Dear FS experts,
>
> I have a question about extracting average cortical thickness from a
> manually created ROI. I am comparing 2 groups, namely PostFort and
> PreFort and my fsgd file appears as the following:
>
> GroupDescriptorFile 1
> Title PostPreFortification
> Class PostFort
> Class PreFort
>
> InputSubject1PostFort
> InputSubject2PostFort
> .
> .
> .
>
> The contrast that I use to compare these groups is [1 -1]. When I
> display the significance map for this contrast I get the following
> image on the left hemisphere:
>
>
>
>
> My first question is, those blue clusters represent regions, where
> thickness is greater in the PreFort group, don't they?
Correct
> Assuming this is correct, I created a label for this region (which
> contains about 3000 vertices) and extracted the thickness value from
> this region for each subject using the following commands. These
> commands are part of scripts in which $subject and $label are defined.
>
>
>
> _to make a label for each subject (the original label was created on
> fsaverage):_
> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label
> --srcsubject fsaverage --trglabel
> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
> --regmethod surface --hemi lh
>
> _to create a stats file of this ROI containing several anatomical
> measures:_
> *mris_anatomical_stats* -f
> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
> $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
>
> _to compile thickness values from all subjects into one table: _
> *aparcstats2table* --hemi lh --subjectsfile
> $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc
> NP_PostMINUSPre_IPS.label --meas thickness --tablefile
> $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt
>
> This table displays the average thickness value of my ROI for each
> subject. Based on this table I calculated the mean thickness for each
> group, which is as the following:
>
> PostFort: 3.043
> PreFort: 2.842
>
> My question is: If this cluster appears blue in the Post>Pre map,
> shouldn't the thickness have been greater in the PreFort group? Or am
> I missing a step?
Not sure. The commands look right. Can you try something else?
mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh
--id 1 --avgwf y.label.dat

This should create a single column of numbers in y.label.dat that
correspond to the mean thickness in the label of each  subject as
ordered in your fsgd file. See if you get similar numbers to your method
doug



>
> Many thanks in advance!
>
> Best,
> Hamdi
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Clara Kühn]

Our IT guy said it could be a software problem since he didn't have the problem 
and the only difference between out computers was the display.
We have these versions at the institute: 

4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
Is the first one the dev version?

Cheers, Clara

- Ursprüngliche Mail -
Von: "Ruopeng Wang" 
An: "Freesurfer support list" 
Gesendet: Dienstag, 3. November 2015 17:57:50
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, 
can you try the dev version of freeview? 

Ruopeng 

On 11/03/2015 11:50 AM, Bruce Fischl wrote: 


Hi Clara 

that doesn't crash for me. Are you sure you ahve write permission to the file? 
And that the disk isn't full? Ruopeng: any other ideas? 

Bruce 

On Tue, 3 Nov 2015, Clara Kühn wrote: 



Hi Bruce, 

I attached the wm.mgz from one of my participants. It happens with any 
participant though. 
What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then 
it crashes with afore mentioned error message. 

Cheers, Clara 

- Ursprüngliche Mail - 
Von: "Bruce Fischl"  
An: "Freesurfer support list"  
Gesendet: Dienstag, 3. November 2015 14:42:25 
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes 

Hi Clara 

can you send us the wm.mgz and tell us exactly what you did to make it 
crash? 

thahks 
Bruce 
On Tue, 3 Nov 2015, Clara Kühn wrote: 



Dear FreeSurfer experts, 

since last week I have the problem that FS (5.3.0) crashes when I try to save 
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
always restore it by renaming the temporary file (wm.mgz~) but it obviously 
doen't save any changes. 

I've tried different computers (same FS version) and on some it works and on 
some the same problem occurs. I just tried it on the 6.0.0beta version and it 
saved like a charm. I would rather, however, keep editing my data with the same 
version. 
Here is the error message I get in the terminal: 

[0]PETSC ERROR: 
 
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range 
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger 
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal 
[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple 
to find memory corruption errors 
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash. 
[0]PETSC ERROR: - Error Message 
 
[0]PETSC ERROR: Signal received! 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 
[0]PETSC ERROR: See docs/changes/index.html for recent updates. 
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. 
[0]PETSC ERROR: See docs/index.html for manual pages. 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
17:22:55 2015 
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
 
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file 
[unset]: aborting job: 
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 
Segmentation fault (core dumped) 

Any idea what it means by Segmentation Violation and how I can fix it?? 
Cheers and thanks in advance! 
Clara Kühn 

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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[pablo najt]

Dear Martin and FS experts.I have a quick query about how to obtain my design 
matrix of group by age from the following matlab command listed in the lme 
wiki. In the wiki example the matrix is created from variables 1 and 2 (group 
by time). X = [ones(length(M),1) M M(:,1).*M(:,2);
In my case I have a combination of variables 1 and 2 for group (relatives of PT 
and PT) and 5 (age).
I would really appreciate if you could kindly advice on how to adapt the 
command above to my design.
Thanks
Pablo
To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Tue, 27 Oct 2015 17:13:51 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}


  

  
  
Hi Pablo,



the sortData function sorts the rows so that entries from the same
subject (in your case same family) are blocked and that within each
block the time variable (2nd parameter specifies which column that
is in your M matrix, in your case the first =1) is increasing. 

It is important, when creating your design matrix X, that ordering
agrees with Y. That is guaranteed if you generate X from M (which is
ordered like Y after the sort command). 



Best, Martin



On 10/27/2015 01:32 PM, pablo najt
  wrote:



  

Thank you for your input. 
I noticed that if I follow literally all the
  steps in the wiki, my data which is ordered by variable
  'family' (instead of subjects, in my case is number of members
  belonging to e.g. family_1) is shuffled. This happens after I
  run the command sortData below. Especially I noticed that ni
  and X do not match sID.
It would be really helpful to know what is this
  command doing. I am wondering whether my data differs in
  number of columns or else and because of this I end with a
  shuffled data. Any suggestion or tips to figure what could be
  happening?
Thanks
Pablo

  

  
  [M, Y, ni] = sortData(M,1,Y,sID)
  


  
To: freesurfer@nmr.mgh.harvard.edu

From: mreu...@nmr.mgh.harvard.edu

Date: Wed, 14 Oct 2015 10:54:41 -0400

Subject: Re: [Freesurfer] A mixed effect model approach
in within subject dataset {Disarmed}



Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)
see


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




hope that helps, Martin





On 10/14/2015 10:43 AM,
  pablo najt wrote:



  

Dear FS experts.
  I have query about a relating to a previous
email (below). I
  am aiming to run a LME analysis on
  cross-sectional data from different families
  and have variable 'family' (number of
  families) as my NI vector. 
  My design has three groups and therefore I am
not able to use qdec. I am running the matlab
commands below and finding some difficulty would
really appreciate if you could help out.
  Thanks
  Pablo
  


  Start analysis as follows:
  

  
  1-Read your label eg.:

  lhcortex = 
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');

  2-Read the data file eg.:

  [lhY, lhmri] = fs_read_Y('lh.thickness.mgh'); 

  
 %-I input the concatenated .mgh 
image from preproc and 
mris_surf2surf---%


  
  3-Fit a vertex-wise lme model with random effects.:

  lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex); 

  
Here I am getting the following problems:
% If I use number of families as my 
ni get the 
following%
  


  

  
lhstats = 

Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

[Douglas N Greve]

It will be in an FS native coordinate system which is not interpretable 
by other software. What you can do is to run mris_convert with the 
--to-scanner option to have it save the coordinates in scanner space. If 
your version does not have the --to-scanner option, then get the version 
below

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert


On 11/03/2015 09:46 AM, Razlighi, Qolamreza R. wrote:
> Thanks Bruce,
> I read in another post that these coordinates in ascii file are in 
> native space. So if I load the original volume in another 
> visualization tool (e.g. fslview), these coordinates should be right 
> on the border of white/gray matter. Is that correct?
> I already checked couple of them but wanted to be sure this is the case.
> Also, if freeview doesn’t get the header information from ascii files, 
> what header info (probably a default one) it uses to plot them? Is 
> there any way we can give those header information separately to freeview?
>
> Best
>
> -- 
> Ray Razlighi, Ph.D.
> Assistant Professor
> Quantitative Neuroimaging Laboratory
> Division of Cognitive Neuroscience
> Department of Neurology
> Columbia University
>
> Alt: razli...@gmail.com 
> Office Phone: 212-342-1352
> Office Fax: 212-342-1838
> Website: http://www.columbia.edu/cu/qnl/
>
> On Nov 2, 2015, at 10:02 AM, Bruce Fischl  > wrote:
>
>> Hi Ray
>>
>> the ascii format is pretty barebones and doesn't have e.g. ras2vox info
>> that freeview uses to display the surfaces properly.  It's for ease of
>> conversion and such.
>>
>> cheers
>> Bruce
>>
>> On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote:
>>
>>> Hi Guys,
>>> Why converting a surface to .asc format changes its spatial 
>>> orientation? Specifically, I have converted lh.while to lh.white.asc 
>>> (using: mris_convert lh.white lh.white.asc) and plot both of them 
>>> using freeview but they are not corresponding. In fact, lh.white 
>>> corresponds to the volume image (e.g orig.mgz) but the lh.white.asc 
>>> doesn't. See the attached screenshot. The red curve is the lh.white.asc.
>>> Any explanation would be greatly appreciated.
>>>
>>> Best
>>>
>>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to 
>> you in error
>> but does not contain patient information, please contact the sender 
>> and properly
>> dispose of the e-mail.
>>
>
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] using ADNI preprocessed files in FS

[Riphagen Joost (NP)]

Hi,

Sorry for the very basic question but I have not been able to find the answer 
in the archives, nor anywhere else.

I want to use ADNI data in FS

ADNI data is available in either original DICOM or has been preprocessed in the 
following manner:

Phillips Systems:

unpreprocessed DICOM
N3 corrected

GE and Siemens systems with transmit-receive head RF coils:

unpreprocessed DICOM
gradwarped
gradwarp plus N3

GE and Siemens systems with receive-only head RF coils:

unpreprocessed DICOM
gradwarped
gradwarp plus B1 plus N3

I reality there are quite a few more options available. Question is which one 
to use best for FS (plan is to rerun in a newer FS version)

I suppose that using the files that are gradwarped and B-1 corrected is 
sensible for using in FS. However the "best" files after quality control have 
been N3 corrected which makes it a lot easier for me to extract these files 
from the database (I need a few hundred, meaning I have many thousands of files 
to extract from).

Would running recon all, but omitting the N3 step be correct ?

Thanks a lot,

JM 

Joost Riphagen, MD
Phd candidate
Maastricht University.




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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] First-level analysis (native vs fsaverage)

[Douglas N Greve]

Resample to the surface and then smooth is better.

On 11/03/2015 01:12 PM, Rodriguez-Thompson, Anais wrote:
> Thanks for your response. In general, is it better practice to run the first 
> level analysis in the native space, and then resample the subjects to 
> fsaverage space during concatenation, or to resample the subjects to 
> fsaverage space during first level analysis?
>
> Best,
> Anais
> 
> 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: Tuesday, November 03, 2015 12:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] First-level analysis (native vs fsaverage)
>
> In the native space analysis the data get smoothed in the 3d volume and
> then projecting to the surface. This is very different from a
> surface-based analysis where you project to the surface and then smooth
> in 2D. For one thing, 5mm FWHM in one analysis is not the same as 5mm
> FWHM in the other. You get much more smoothing in the volume at 5mm than
> you do on the surface. Why one is better than the other is hard to say.
> You might try cranking up the smoothing for the surface-based analysis.
>
> doug
>
>
> On 11/02/2015 04:29 PM, Rodriguez-Thompson, Anais wrote:
>> Hi freesurfer experts,
>>
>> I have a question about how running first-level analyses in either native 
>> space or fsaverage space changes activation. My original analysis was a 
>> per-session analysis run on native space.  The command used to make the 
>> analysis was
>>
>> ANALYSIS 1:
>> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm 
>> slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt 
>> -native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 
>> -refeventdur 2
>>
>> However, my lab was interested in running our analyses -per-run, so I 
>> created a new per-run analysis on the fsaverage brain using the command:
>>
>> ANALYSIS 2:
>> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915_lh -TR 2 
>> -paradigm slopepar -event-related -runlistfile runlistfile -tpef 
>> tpef_1.5mm.txt -surface fsaverage lh -fwhm 5 -per-run -timewindow 20 -TER 2 
>> -nconditions 9 -gammafit 2.25 1.25 -refevendur 2 -fsd bold
>>
>> The group maps for the two looked comparable. However, I covaried those maps 
>> with performance on our task. The maps looked significantly different, and 
>> while 9 cluster survived MC correction from analysis 1 (3 LH, 6 RH), only 3 
>> survived MC correction from analysis 2 (0 LH, 2 RH).
>>
>> I thought that the difference could have been due to per-run vs. per-session 
>> MC, but I created a test analysis (per-session, fsaverage space), and this 
>> analysis looked more like the 2nd analysis than the 1st, leading me to 
>> believe that the difference in activation was due to running the first-level 
>> analysis on fsaverage space rather than native space.
>>
>> The command I used for the test analysis was: mkanalysis-sess -analysis 
>> TEST_fsaverage_persession_lh -TR 2 -paradigm slopepar -surface fsaverage lh 
>> -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
>> -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 
>> -fwhm 5 -per-session
>>
>> Do you know why running first-level analyses on fsaverage space rather than 
>> native space would decrease activation effects, leading to fewer significant 
>> clusters after MC correction?
>>
>> I've attached a pdf file with the maps in question.
>>
>> Thanks,
>> Anais
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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Re: [Freesurfer] First-level analysis (native vs fsaverage)

[Douglas N Greve]

No way to know what smoothing level is optimal without actually doing 
the smoothing


On 11/03/2015 02:22 PM, Rodriguez-Thompson, Anais wrote:
> Great, thank you. In terms of smoothing, I don't want to arbitrarily increase 
> smoothing to find effects. Is there an optimal amount of smoothing that 
> should be performed on the surface?
>
> Thanks,
> Anais
> 
> 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: Tuesday, November 03, 2015 1:20 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] First-level analysis (native vs fsaverage)
>
> Resample to the surface and then smooth is better.
>
> On 11/03/2015 01:12 PM, Rodriguez-Thompson, Anais wrote:
>> Thanks for your response. In general, is it better practice to run the first 
>> level analysis in the native space, and then resample the subjects to 
>> fsaverage space during concatenation, or to resample the subjects to 
>> fsaverage space during first level analysis?
>>
>> Best,
>> Anais
>> 
>> 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: Tuesday, November 03, 2015 12:50 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] First-level analysis (native vs fsaverage)
>>
>> In the native space analysis the data get smoothed in the 3d volume and
>> then projecting to the surface. This is very different from a
>> surface-based analysis where you project to the surface and then smooth
>> in 2D. For one thing, 5mm FWHM in one analysis is not the same as 5mm
>> FWHM in the other. You get much more smoothing in the volume at 5mm than
>> you do on the surface. Why one is better than the other is hard to say.
>> You might try cranking up the smoothing for the surface-based analysis.
>>
>> doug
>>
>>
>> On 11/02/2015 04:29 PM, Rodriguez-Thompson, Anais wrote:
>>> Hi freesurfer experts,
>>>
>>> I have a question about how running first-level analyses in either native 
>>> space or fsaverage space changes activation. My original analysis was a 
>>> per-session analysis run on native space.  The command used to make the 
>>> analysis was
>>>
>>> ANALYSIS 1:
>>> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 
>>> -paradigm slopepar -event-related -runlistfile runlistfile -tpef 
>>> tpef_1.5mm.txt -native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 
>>> -gammafit 2.25 1.25 -refeventdur 2
>>>
>>> However, my lab was interested in running our analyses -per-run, so I 
>>> created a new per-run analysis on the fsaverage brain using the command:
>>>
>>> ANALYSIS 2:
>>> mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915_lh -TR 2 
>>> -paradigm slopepar -event-related -runlistfile runlistfile -tpef 
>>> tpef_1.5mm.txt -surface fsaverage lh -fwhm 5 -per-run -timewindow 20 -TER 2 
>>> -nconditions 9 -gammafit 2.25 1.25 -refevendur 2 -fsd bold
>>>
>>> The group maps for the two looked comparable. However, I covaried those 
>>> maps with performance on our task. The maps looked significantly different, 
>>> and while 9 cluster survived MC correction from analysis 1 (3 LH, 6 RH), 
>>> only 3 survived MC correction from analysis 2 (0 LH, 2 RH).
>>>
>>> I thought that the difference could have been due to per-run vs. 
>>> per-session MC, but I created a test analysis (per-session, fsaverage 
>>> space), and this analysis looked more like the 2nd analysis than the 1st, 
>>> leading me to believe that the difference in activation was due to running 
>>> the first-level analysis on fsaverage space rather than native space.
>>>
>>> The command I used for the test analysis was: mkanalysis-sess -analysis 
>>> TEST_fsaverage_persession_lh -TR 2 -paradigm slopepar -surface fsaverage lh 
>>> -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
>>> -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 
>>> -fwhm 5 -per-session
>>>
>>> Do you know why running first-level analyses on fsaverage space rather than 
>>> native space would decrease activation effects, leading to fewer 
>>> significant clusters after MC correction?
>>>
>>> I've attached a pdf file with the maps in question.
>>>
>>> Thanks,
>>> Anais
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> 

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in 
[mydata}/cope7ACroi_rh.osgm.rfx.

There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), and 
even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, gammavar, 
mask, and sig) but no rh.cope7.mgh.

Thanks for going back and forth about this,

Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

> The correct command line is
>
> --cache 4 neg --cache-label AC
>
> On 11/03/2015 03:36 PM, s...@u.washington.edu wrote:
>> Hi Doug,
>>
>>
>>
>> So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot
>> find any documentation about what to put instead of --grf), as in
>>
>> mri_glmfit-sim --glmdir
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx
>> --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces
>>
>> I get back "ERROR: Flag 4 is unrecognized."
>>
>> If I try just --cache instead of --cache-label AC, I get back "ERROR:
>> cannot find
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh"
>>
>> Any thoughts?
>>
>> Many thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> The fwhm.dat file was in the right place. You passed the wrong folder to
>>> mri_glmfit-sim. You should pass it
>>>
>>> cope7ACroi_rh.osgm.rfx
>>>
>>> doug
>>>
>>>
>>> On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
 It's:

 mri_glmfit --y
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh
 --osgm --glmdir
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
 --surf fsaverage lh --label
 /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label

 fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than
 [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also
 happened for some other files needed and I moved them. Is the
 problem something in my mri_glmfit command?

 Susan

 On Tue, 3 Nov 2015, Douglas N Greve wrote:

> it cannot find this file
>
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>
>
> which should have been created by mri_glmfit. What is your mri_glmfit
> command line?
>
> Also, don't use --grf, that is for volumes only
>
>
> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>> Hi DOug,
>>
>> doug.log is attached
>>
>> the bash equivalent for |& is 2>&1 |
>>
>> thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm
>>> not
>>> sure what the bash equivalent is. Maybe |2 instead of |&
>>> perhaps some bash experts can weigh in
>>>
>>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
 Hi Doug,

 Do you mean:

 mri_glmfit-sim --debug --glmdir
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm

 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
 doug.log?

 When I tried running the same code with |& tee doug.log at the end,
 I kept getting:

 syntax error near unexpected token `&'

 Thanks,
 Susan

 On Tue, 3 Nov 2015, Douglas N Greve wrote:

> Can you run
>
> mri_glmfit-sim --debug --glmdir [my data
> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
> --cwpvalthresh 0.05 --2space |& tee doug.log
>
> and send me doug.log?
>
>
>
>
> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>> Hi experts,
>>
>> I am having trouble performing a Monte Carlo correction using
>> mri_glmfit-sim.
>>
>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>> mris_preproc. I then ran mri_glmfit on the data.
>>
>> I want to do my analysis/correction only in auditory cortex (AC)
>> so I did my own simulation in AC of each hemisphere using
>> mri_mcsim (as per
>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>
>> So far, so good.
>>
>> But when I try to run:
>>
>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>
>> I get "fwhm: Undefined variable." I tried adding --fwhm-override
>> 5, but it didn't help.
>>
>> Any thoughts? Also, can you clarify which comparison neg vs pos
>> will give me?
>>
>> Thank you,
>>
>> Susan McLaughlin, PhD
>> Research Scientist
>> Laboratory for Auditory Brain 

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

[pablo najt]

Thank you Martin.
My intention was not to enquire about advice on the statistical model but 
instead on how to run the matlab commad with two experimental groups.
My decision is to test group by age interaction for each group. The way to 
proceed for this would be to create two separate matrices?
Thanks
Pablo

To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Tue, 3 Nov 2015 12:10:17 -0500
Subject: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}


  

  
  
Dear Pablo,

maybe what you want is a group x age interaction for each of those
groups? (so 1x5 and 2x5)?

Not sure. It is your hypothesis, your model and we usually don't
give advise on model building. Since you have a special case (within
family analysis) I would recommend you try to get some advise from a
bio-statistician, if unsure what you are doing.



Best, Martin





On 11/03/2015 12:01 PM, pablo najt
  wrote:



  
  Dear Martin and FS experts.
I have a quick query about how to obtain my design matrix
  of group by age from the following matlab command
  listed in the lme wiki. In the wiki example the matrix is
  created from variables 1 and 2 (group by time).

   X = [ones(length(M),1) M M(:,1).*M(:,2);
  

  

In my case I have a combination
  of variables 1 and 2 for group (relatives of PT and PT) and 5
  (age).

I would really appreciate if you
  could kindly advice on how to adapt the command above to my
  design.

Thanks

Pablo


  
To: freesurfer@nmr.mgh.harvard.edu

From: mreu...@nmr.mgh.harvard.edu

Date: Tue, 27 Oct 2015 17:13:51 -0400

Subject: Re: [Freesurfer] A mixed effect model approach in
within subject dataset {Disarmed}



Hi Pablo,



the sortData function sorts the rows so that entries from
the same subject (in your case same family) are blocked and
that within each block the time variable (2nd parameter
specifies which column that is in your M matrix, in your
case the first =1) is increasing. 

It is important, when creating your design matrix X, that
ordering agrees with Y. That is guaranteed if you generate X
from M (which is ordered like Y after the sort command). 



Best, Martin



On 10/27/2015 01:32 PM,
  pablo najt wrote:



  

Thank you for your input. 
I noticed that if I follow literally all
  the steps in the wiki, my data which is ordered by
  variable 'family' (instead of subjects, in my case is
  number of members belonging to e.g. family_1) is
  shuffled. This happens after I run the command
  sortData below. Especially I noticed that ni and X do
  not match sID.
It would be really helpful to know what
  is this command doing. I am wondering whether my data
  differs in number of columns or else and because of
  this I end with a shuffled data. Any suggestion or
  tips to figure what could be happening?
Thanks
Pablo

  

  
  [M, Y, ni] = sortData(M,1,Y,sID)
  


  
To: freesurfer@nmr.mgh.harvard.edu

From: mreu...@nmr.mgh.harvard.edu

Date: Wed, 14 Oct 2015 10:54:41 -0400

Subject: Re: [Freesurfer] A mixed effect model
approach in within subject dataset {Disarmed}



Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)
see


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




hope that helps, Martin





On 10/14/2015
  10:43 AM, pablo najt wrote:



  

Dear FS experts.
  I have query about a relating to a
previous email (below). I am aiming
  to run a LME analysis on
  

[Freesurfer] Post-Doctoral position in brain imaging – University of Geneva {Disarmed}

[Narly Golestani]

?Applications are invited for a Post-Doctoral position in the Brain and 
Language Lab (www.brainandlanguagelab.org) 
at the University of Geneva.  The position is for 2 years (or more), and will 
be at the new Biotech Campus (http://www.campusbiotech.ch/en/).


Candidates should have a degree in Psychology and/or Cognitive Neuroscience, 
and should have a solid background in statistics and in the analysis of 
functional magnetic resonance imaging data. The projects will include brain 
imaging and behavioural studies on multilingualism and expertise, with a focus 
on executive skills, attention and statistical/language learning.


The salary is competitive, starting salary at ~ 69, 000 CHF/year (~ 81, 000 
CHF/year as of August 2016) depending on experience.


The position is available immediately, and applications will be considered 
until the position is filled.  Informal inquiries can be addressed to Narly 
Golestani (narly.golest...@unige.ch).   Applications including a CV, a 
statement of research interests, and the names and full contact details of 
three referees should be sent to: 
narly.golest...@unige.ch.

?-
Brain and Language Lab
Department of Clinical Neuroscience
Biotech Campus
9 Chemin des Mines,
1202 Genève
+41 22 379 53 52
http://www.brainandlanguagelab.org
-

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[Freesurfer] Adding more than 2 covariates in QDEC

[Deborrah Castillo]

I wanted to ask if it is possible to run analysis in QDEC with more than 2
covariates for examples, instead of Age, I wanted to add depression scores
or race? At the moment my qdec table has two groups, two covariates...

Class Group1
Class Group2
Variables Age PainMeasure

If it is not possible, what is other alternate method would you suggest I
could use to run analysis to look at group differences in brain measures
with covarying for Age and Race / Depression Score in FreeSurfer?

Thank you.

Aloha,
Deborrah
-- 
-- 
University of Hawaii
John A. Burns School of Medicine
Department of Medicine
Neuroscience and Magnetic Resonance Research Program
Queens Medical Center, 7th Floor UH Tower
1356 Lusitana Street
Honolulu, HI 96813
Tel:+1-808-586-7488
Tel: +1808-586-7459

Fax:+1808-586-7465
Web: http://hawaii.edu/mri/home_v6.htm
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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.

Re: [Freesurfer] Freesurfer 6.0

[Bruce Fischl]

Hi Matt
this would be a beta - the new version isn't ready to be distributed yet 
(although we are getting closer)

Bruce
On Tue, 3 Nov 2015, Hoptman, Matthew wrote:



Hi all,
I can see a link for Freesurfer 6.0 on the website, but when I click on it
to download, it just blinks at me.  I also tried to ftp to your ftp site,
and unfortunately, I got the message

421 Proxy is closed (unknown user location). 

 

Could you please tell me how I could get the new version of Freesurfer?

Thanks,

Matt

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
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[Freesurfer] Fwd: visualizing paths stats by voxel

[Janosch Linkersdörfer]

> Begin forwarded message:
> 
> From: Janosch Linkersdörfer 
> Subject: Re: visualizing paths stats by voxel
> Date: 3 Nov 2015 09:37:48 CET
> To: Anastasia Yendiki 
> Cc: freesurfer@nmr.mgh.harvard.edu
> 
> Hi Anastasia and list,
> 
> sorry, I just now got around to testing out the new build of dmri_paths you 
> sent me. Sadly, the results look about the same:
> 
> 
> 
> Here the path stats file for the left SLFt:
#!ascii label
53
1 -50.1205 2.05458 20.1324 0
2 -49.0568 1.40645 20.8743 0
3 -47.024 0.495407 22.0052 0
4 -46.0977 -0.262421 22.1583 0
5 -44.4218 -1.30921 22.7764 0
6 -43.2968 -1.3833 23.3134 0
7 -41.2815 -1.94728 24.0532 0
8 -40.1774 -2.62188 24.8471 0
9 -39.143 -3.68113 25.4572 0
10 -38.0383 -4.9254 26.3159 0
11 -37.2828 -6.68602 27.0788 0
12 -36.5155 -8.22572 27.6033 0
13 -35.7584 -10.1152 28.2235 0
14 -35.3687 -11.6727 28.7698 0
15 -34.7487 -13.5948 29.3084 0
16 -34.0861 -15.8398 29.7752 0
17 -33.9133 -17.4602 30.2452 0
18 -33.5104 -19.6399 30.5545 0
19 -33.3487 -21.7044 30.7416 0
20 -32.9916 -23.9215 30.9002 0
21 -31.4122 -26.7961 31.088 0
22 -31.2762 -28.9119 31.2611 0
23 -31.1289 -31.2752 30.8061 0
24 -30.8814 -33.1307 30.5293 0
25 -29.5803 -36.1004 30.7024 0
26 -27.2789 -39.691 31.0453 0
27 -16.641 -48.8283 35.0155 0
28 -16.5297 -49.7169 34.264 0
29 -16.5432 -50.9074 32.951 0
30 -16.7235 -51.6755 31.9552 0
31 -16.9983 -52.2055 30.3891 0
32 -17.3004 -52.6851 28.9923 0
33 -17.6197 -53.0619 27.5988 0
34 -17.9982 -53.2888 26.4068 0
35 -18.4567 -53.4429 25.1512 0
36 -18.9968 -53.6854 23.6134 0
37 -19.8229 -53.7862 21.8063 0
38 -20.4389 -54.1143 20.5701 0
39 -21.1905 -54.2719 19.3752 0
40 -21.7858 -54.4113 18.3986 0
41 -23.0093 -54.3412 16.9705 0
42 -24.1073 -54.5756 15.7345 0
43 -25.302 -54.5493 14.8829 0
44 -26.706 -54.7199 13.7208 0
45 -27.1493 -55.0881 13.003 0
46 -28.5131 -55.2495 12.4195 0
47 -25.8897 -58.0703 15.0856 0
48 -22.3874 -60.6226 18.735 0
49 -14.1178 -65.6153 25.9802 0
50 -9.17648 -68.7466 30.4727 0
51 3.31329 -77.2664 41.7526 0
52 22.0756 -89.6051 55.8685 0
53 19.4398 -88.1799 54.2416 0
> 
> 
> What could be the problem?! I think I did what you suggested:
> 
> - install the new version of dmri_paths 
> (https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it 
> executable
> - rerun trac-all -path for the subjects with only one time point
> - rerun trac-all -stat for all subjects
> 
> Also: Is that problem only a visualization problem, or does it also mean that 
> the values I get for a participant at a specific part of a tract are not 
> aligned and I cannot analyze the data in that way?
> 
> Thanks for your help!!
> 
> Best,
> 
> Janosch
> 
> 
>> On 20 Aug 2015, at 21:35, Anastasia Yendiki  
>> wrote:
>> 
>> 
>> Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of 
>> dmri_paths tomorrow. You'll have to replace your copy of 
>> $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" only 
>> for the subjects that have 1 time point. Then rerun "trac-all -stat" with 
>> all subjects together. And then tell us what other problem you find :)
>> 
>> Best,
>> a.y
>> 
>> On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote:
>> 
>>> Hey Anastasia,
>>> 
 Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki 
 :
 
 
 Hi Janosch - There is a bug in how the output paths are saved when 
 longitudinal TRACULA is run with one time point only. I'm working on a fix.
>>> 
>>> OK, then I'm relieved that it isn't an error on my side. Thank you very 
>>> much for looking into it!
>>> 
 In the meantime, you can try your analysis with the subjects that have 
 multiple time points and you won't be affected by this problem. I can see 
 that the subjects with a single time point are about 1/3 of your sample, 
 and so you may not want to drop them completely.
>>> 
>>> Yeah, it's children's data, so I'm happy about every measurement we got. 
>>> I'll be waiting for the fixed script to be able to include all subjects in 
>>> the analysis...
>>> 
 
 Thank you for trying things that nobody else has tried and finding these 
 bugs!
>>> 
>>> Somebody has to be the first, eh? :)
>>> 
>>> Thank you very much,
>>> 
>>> Janosch
>>> 
 
 More soon,
 a.y
 
 On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote:
 
> Hey Anastasia,
> 
> thanks for looking into this.
> 
>> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki 
>> :
>> 
>> 
>> Hi Janosch - Looking at the stats files of your subjects, just by a 
>> quick count of the number of lines, I see that there are some subjects 
>> that have only 1 time point and some that have multiple time points, and 
>> that the pathstats.byvoxel.txt files have different lengths between 
>> those two types of subjects.
>> 
>> I suspect that the strange average 

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

[Eryilmaz, H. Hamdi]

Hi Doug, 

I used the following command for mris_preproc to concatenate the maps from 214 
subjects: 

mris_preproc --f /$SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --target 
fsaverage --hemi lh --meas thickness --out 
/$SUBJECTS_DIR/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_map.mgh

Does the order in the subject list file I specified in the --f flag above need 
to be exactly the same as in the fsgd files I later used (below) to compare the 
groups? If so, that might be the source of the problem. Here's my mri_glmfit 
command: 

mri_glmfit --y 
/$SUBJECTS_DIR/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_map.mgh 
--fsgd /$SUBJECTS_DIR/fsgd/RPDR_083115/102PostFort_Minus_112PreFort.fsgd --C 
/$SUBJECTS_DIR/fsgd/Top_Minus_Bottom.mtx --glmdir 
/cluster/deplin/chris/data/Subjects/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_fwhm22
 --surf fsaverage lh --fwhm 22 --no-prune

Thanks!
Hamdi



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: Tuesday, November 03, 2015 2:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

The y.mgh file is created by your call to mris_preproc (or by a
subsequent call to mri_surf2surf for smoothing). The order of the
subjects depends on how you called mris_preproc (which should match that
in the fsgd file or else everything will be bogus). The y.mgh file
contains all the subjects in fsaverage space, so you don't need to run
it for each subject or resample back into native space

On 11/03/2015 02:29 PM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> Thanks for the reply. Sure I will try this command. But as it is now, how 
> will mri_segstats know the order in the fsgd file? Also, this command needs 
> to run for each subject, right? Then, which input file should I use for the 
> --i flag?
>
> mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh--id 1 
> --avgwf y.label.dat
>
>
> Thanks a lot!
> Hamdi
>
> 
> 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: Tuesday, November 03, 2015 2:01 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a 
> ROI
>
> On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
>> Sorry, the figures I inserted in the text did not appear in the email.
>> I attach them now.
>>
>> Best,
>> Hamdi
>>
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H.
>> Hamdi [hamdi.eryil...@mgh.harvard.edu]
>> *Sent:* Friday, October 30, 2015 1:32 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] cortical thickness - comparing two groups
>> within a ROI
>>
>> Dear FS experts,
>>
>> I have a question about extracting average cortical thickness from a
>> manually created ROI. I am comparing 2 groups, namely PostFort and
>> PreFort and my fsgd file appears as the following:
>>
>> GroupDescriptorFile 1
>> Title PostPreFortification
>> Class PostFort
>> Class PreFort
>>
>> InputSubject1PostFort
>> InputSubject2PostFort
>> .
>> .
>> .
>>
>> The contrast that I use to compare these groups is [1 -1]. When I
>> display the significance map for this contrast I get the following
>> image on the left hemisphere:
>>
>>
>>
>>
>> My first question is, those blue clusters represent regions, where
>> thickness is greater in the PreFort group, don't they?
> Correct
>> Assuming this is correct, I created a label for this region (which
>> contains about 3000 vertices) and extracted the thickness value from
>> this region for each subject using the following commands. These
>> commands are part of scripts in which $subject and $label are defined.
>>
>>
>>
>> _to make a label for each subject (the original label was created on
>> fsaverage):_
>> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label
>> --srcsubject fsaverage --trglabel
>> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
>> --regmethod surface --hemi lh
>>
>> _to create a stats file of this ROI containing several anatomical
>> measures:_
>> *mris_anatomical_stats* -f
>> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
>> $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
>>
>> _to compile thickness values from all subjects into one table: _
>> *aparcstats2table* --hemi lh --subjectsfile
>> $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc
>> NP_PostMINUSPre_IPS.label --meas thickness --tablefile
>> $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt
>>
>> This table displays the average thickness value of my ROI 

Re: [Freesurfer] Adding more than 2 covariates in QDEC

[Douglas N Greve]

you will have to use the command-line stream. Check out the tutorials we 
have on line. You'll need to create an FSGD file (example on the wiki), 
then run mris_preproc, then mri_surf2surf to smooth, then mri_glmfit, 
then mri_glmfit-sim (to correct for multiple comparisons).
doug

On 11/03/2015 03:36 PM, Deborrah Castillo wrote:
> I wanted to ask if it is possible to run analysis in QDEC with more 
> than 2 covariates for examples, instead of Age, I wanted to add 
> depression scores or race? At the moment my qdec table has two groups, 
> two covariates...
> Class Group1
> Class Group2
> Variables Age PainMeasure
> If it is not possible, what is other alternate method would you 
> suggest I could use to run analysis to look at group differences in 
> brain measures with covarying for Age and Race / Depression Score in 
> FreeSurfer?
>
> Thank you.
>
> Aloha,
> Deborrah
> -- 
> -- 
> University of Hawaii
> John A. Burns School of Medicine
> Department of Medicine
> Neuroscience and Magnetic Resonance Research Program
> Queens Medical Center, 7th Floor UH Tower
> 1356 Lusitana Street
> Honolulu, HI 96813
> Tel:+1-808-586-7488 
> Tel: +1808-586-7459 
>
> Fax:+1808-586-7465 
> Web: http://hawaii.edu/mri/home_v6.htm
>
>
>
> ___
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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] Surface-based registration

[Bruce Fischl]

Hi Ray

the -1 means that the target is a single surface and not an atlas, but 
the registration is still nonlinear. The variances will all be 1 so you 
may have to play with the weights in the energy functional. We don't do 
this very much and it probably defaults to quite rigid. Try reducing the 
weight on the metric preservation term (e.g. -dist .25) if you want it to 
be more nonlinear


cheers
Bruce

On Tue, 3 Nov 2015, Razlighi, Qolamreza R. wrote:


Hi Guys,
I read in the sidenote here
(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) that
inter-subject surface base registration using mris_register and -1 flag
performs a sort of rigid registration. So I tried it between two of my
subjects with the command below

mris_register -1 -curv P1639/FreeSurferClean/surf/lh.sphere
P1639/FreeSurferClean/surf/lh.sphere lh.sphere3.reg 

and got the results (see the attachment). It is clear that the registration
output is just a shifted version of the source. Having this confirmed I want
to know if there is any way to force the mris_register to perform a complete
non-linear surface based registration for inter-subjects registration the
same way it does for template.

I have to mention that I visualize the lh.sphere3.reg using freeview and
loaded the sane lh.curv on that surface. I hope I’m not doing anything
stupid.

  
[IMAGE]

Best
-- 
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University

Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/


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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

The correct command line is

--cache 4 neg --cache-label AC

On 11/03/2015 03:36 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
>
>
> So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot 
> find any documentation about what to put instead of --grf), as in
>
> mri_glmfit-sim --glmdir 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx 
> --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces
>
> I get back "ERROR: Flag 4 is unrecognized."
>
> If I try just --cache instead of --cache-label AC, I get back "ERROR: 
> cannot find 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh"
>
> Any thoughts?
>
> Many thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> The fwhm.dat file was in the right place. You passed the wrong folder to
>> mri_glmfit-sim. You should pass it
>>
>> cope7ACroi_rh.osgm.rfx
>>
>> doug
>>
>>
>> On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
>>> It's:
>>>
>>> mri_glmfit --y 
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh 
>>> --osgm --glmdir 
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
>>>  
>>> --surf fsaverage lh --label 
>>> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
>>>
>>> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than 
>>> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also 
>>> happened for some other files needed and I moved them. Is the 
>>> problem something in my mri_glmfit command?
>>>
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 it cannot find this file

 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
  


 which should have been created by mri_glmfit. What is your mri_glmfit
 command line?

 Also, don't use --grf, that is for volumes only


 On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
> Hi DOug,
>
> doug.log is attached
>
> the bash equivalent for |& is 2>&1 |
>
> thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm 
>> not
>> sure what the bash equivalent is. Maybe |2 instead of |&
>> perhaps some bash experts can weigh in
>>
>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
>>> Hi Doug,
>>>
>>> Do you mean:
>>>
>>> mri_glmfit-sim --debug --glmdir
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>>>  
>>>
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
>>> doug.log?
>>>
>>> When I tried running the same code with |& tee doug.log at the end,
>>> I kept getting:
>>>
>>> syntax error near unexpected token `&'
>>>
>>> Thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 Can you run

 mri_glmfit-sim --debug --glmdir [my data
 dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
 --cwpvalthresh 0.05 --2space |& tee doug.log

 and send me doug.log?




 On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
> Hi experts,
>
> I am having trouble performing a Monte Carlo correction using
> mri_glmfit-sim.
>
> My data were sampled to fsaverage and smoothed at fwhm 5, using
> mris_preproc. I then ran mri_glmfit on the data.
>
> I want to do my analysis/correction only in auditory cortex (AC)
> so I did my own simulation in AC of each hemisphere using
> mri_mcsim (as per
> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>
> So far, so good.
>
> But when I try to run:
>
> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>
> I get "fwhm: Undefined variable." I tried adding --fwhm-override
> 5, but it didn't help.
>
> Any thoughts? Also, can you clarify which comparison neg vs pos
> will give me?
>
> Thank you,
>
> Susan McLaughlin, PhD
> Research Scientist
> Laboratory for Auditory Brain Sciences & Neuroengineering
> Institute for Learning & Brain Sciences (I-LABS)
> Portage Bay Bldg. Room 204
> University of Washington, Box 357988
> Seattle, WA 98195-7988
>
> Ph: (206) 616-0102 Fx: (206) 221-6472
> Cell: 206-850-8638
> E-mail: s...@uw.edu
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] Freesurfer 6.0

[Z K]

It must be an issue with your browser. Try using either of the following 
commands (depending on your platform) in a terminal window.

Linux:
wget 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz

Mac OSX:
curl -O 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Darwin-OSX-stable-v6-beta-20151015.dmg

-Zeke

On 11/03/2015 03:44 PM, Hoptman, Matthew wrote:
> Hi all,
> I can see a link for Freesurfer 6.0 on the website, but when I click on
> it to download, it just blinks at me.  I also tried to ftp to your ftp
> site, and unfortunately, I got the message
>
> 421 Proxy is closed (unknown user location).
>
> Could you please tell me how I could get the new version of Freesurfer?
>
> Thanks,
>
> Matt
>
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
> recipient. It may contain confidential information which is legally
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[Freesurfer] Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors UCSD

[Leyden, Kelly]

Dear Freesurfers,

I am writing on behalf of Dr. Carrie McDonald to advertise a Postdoctoral 
position with our lab at UC San Diego.

Location:  UCSD Multimodal Imaging Laboratory (MMIL)
   UCSD Center for Translational Imaging and Precision Medicine (CTIPM)

Start date:  Flexible, but no later than January 2016

Seeking a full-time postdoctoral scholar to work with a multidisciplinary team 
of scientists on projects related to the use of multimodal imaging for 
improving cognitive and health outcomes in patients with epilepsy and primary 
brain tumors.

Our multimodal imaging team includes full-time faculty from Psychiatry, 
Radiology, Neurosciences, and Radiation Oncology.   This group of researchers 
and clinical investigators are primarily focused on integrating research 
imaging tools into the clinical work flow to directly and immediately improve 
patient outcomes.   The scholar will work closely with other postdoctoral 
fellows, medical residents, graduate students, research assistants, and faculty 
members to help develop methods, analyze structural, diffusion, and functional 
(fMRI) imaging data, prepare manuscripts and assist with grant applications.

The fellow should have strong programming (i.e., MATLAB) and writing skills, 
experience in neuroimaging or a related field, and a strong interest in pursing 
an academic career path.  Applicants with a strong background in 
bioengineering, cognitive science, and/or experience working with neurological 
populations are encouraged to apply.

Please send CV and cover letter to Dr. Carrie McDonald 
(camcdon...@ucsd.edu).

Thank you,
Kelly

Kelly Leyden, MRes
Neuroimaging Research Associate
Multimodal Imaging Laboratory
University of California San Diego
kley...@ucsd.edu
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

The fwhm.dat file was in the right place. You passed the wrong folder to 
mri_glmfit-sim. You should pass it

cope7ACroi_rh.osgm.rfx

doug


On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
> It's:
>
> mri_glmfit --y 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh 
> --osgm --glmdir 
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
>  --surf fsaverage lh --label 
> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
>
> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than 
> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for 
> some other files needed and I moved them. Is the problem something in my 
> mri_glmfit command?
>
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> it cannot find this file
>>
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>>
>> which should have been created by mri_glmfit. What is your mri_glmfit
>> command line?
>>
>> Also, don't use --grf, that is for volumes only
>>
>>
>> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>>> Hi DOug,
>>>
>>> doug.log is attached
>>>
>>> the bash equivalent for |& is 2>&1 |
>>>
>>> thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
 sure what the bash equivalent is. Maybe |2 instead of |&
 perhaps some bash experts can weigh in

 On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
> Do you mean:
>
> mri_glmfit-sim --debug --glmdir
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
> doug.log?
>
> When I tried running the same code with |& tee doug.log at the end,
> I kept getting:
>
> syntax error near unexpected token `&'
>
> Thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> Can you run
>>
>> mri_glmfit-sim --debug --glmdir [my data
>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
>> --cwpvalthresh 0.05 --2space |& tee doug.log
>>
>> and send me doug.log?
>>
>>
>>
>>
>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>>> Hi experts,
>>>
>>> I am having trouble performing a Monte Carlo correction using
>>> mri_glmfit-sim.
>>>
>>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>>> mris_preproc. I then ran mri_glmfit on the data.
>>>
>>> I want to do my analysis/correction only in auditory cortex (AC)
>>> so I did my own simulation in AC of each hemisphere using
>>> mri_mcsim (as per
>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>>
>>> So far, so good.
>>>
>>> But when I try to run:
>>>
>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>>
>>> I get "fwhm: Undefined variable." I tried adding --fwhm-override
>>> 5, but it didn't help.
>>>
>>> Any thoughts? Also, can you clarify which comparison neg vs pos
>>> will give me?
>>>
>>> Thank you,
>>>
>>> Susan McLaughlin, PhD
>>> Research Scientist
>>> Laboratory for Auditory Brain Sciences & Neuroengineering
>>> Institute for Learning & Brain Sciences (I-LABS)
>>> Portage Bay Bldg. Room 204
>>> University of Washington, Box 357988
>>> Seattle, WA 98195-7988
>>>
>>> Ph: (206) 616-0102 Fx: (206) 221-6472
>>> Cell: 206-850-8638
>>> E-mail: s...@uw.edu
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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
>> 

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[smcl]

It's:

mri_glmfit --y 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh --osgm 
--glmdir 
/Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
 --surf fsaverage lh --label 
/Applications/freesurfer/subjects/fsaverage/label/lh.AC.label

fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than 
[MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also happened for 
some other files needed and I moved them. Is the problem something in my 
mri_glmfit command?

Susan

On Tue, 3 Nov 2015, Douglas N Greve wrote:

>
> it cannot find this file
>
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>
> which should have been created by mri_glmfit. What is your mri_glmfit
> command line?
>
> Also, don't use --grf, that is for volumes only
>
>
> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>> Hi DOug,
>>
>> doug.log is attached
>>
>> the bash equivalent for |& is 2>&1 |
>>
>> thanks,
>> Susan
>>
>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>
>>> I meant &. The & works for tcsh (or csh). Are you using bash? I'm not
>>> sure what the bash equivalent is. Maybe |2 instead of |&
>>> perhaps some bash experts can weigh in
>>>
>>> On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
 Hi Doug,

 Do you mean:

mri_glmfit-sim --debug --glmdir
 /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
 --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
 doug.log?

 When I tried running the same code with |& tee doug.log at the end,
 I kept getting:

 syntax error near unexpected token `&'

 Thanks,
 Susan

 On Tue, 3 Nov 2015, Douglas N Greve wrote:

> Can you run
>
> mri_glmfit-sim --debug --glmdir [my data
> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
> --cwpvalthresh 0.05 --2space |& tee doug.log
>
> and send me doug.log?
>
>
>
>
> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>> Hi experts,
>>
>> I am having trouble performing a Monte Carlo correction using
>> mri_glmfit-sim.
>>
>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>> mris_preproc. I then ran mri_glmfit on the data.
>>
>> I want to do my analysis/correction only in auditory cortex (AC)
>> so I did my own simulation in AC of each hemisphere using
>> mri_mcsim (as per
>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>
>> So far, so good.
>>
>> But when I try to run:
>>
>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space
>>
>> I get "fwhm: Undefined variable." I tried adding --fwhm-override
>> 5, but it didn't help.
>>
>> Any thoughts? Also, can you clarify which comparison neg vs pos
>> will give me?
>>
>> Thank you,
>>
>> Susan McLaughlin, PhD
>> Research Scientist
>> Laboratory for Auditory Brain Sciences & Neuroengineering
>> Institute for Learning & Brain Sciences (I-LABS)
>> Portage Bay Bldg. Room 204
>> University of Washington, Box 357988
>> Seattle, WA 98195-7988
>>
>> Ph: (206) 616-0102 Fx: (206) 221-6472
>> Cell: 206-850-8638
>> E-mail: s...@uw.edu
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>>
>>> --
>>> Douglas N. Greve, 

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

[Douglas N Greve]

Yes, it must be exactly the same. You can pass mris_preproc your fsgd 
file instead of using --f. This assures that the order will be the same

On 11/03/2015 02:52 PM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> I used the following command for mris_preproc to concatenate the maps from 
> 214 subjects:
>
> mris_preproc --f /$SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --target 
> fsaverage --hemi lh --meas thickness --out 
> /$SUBJECTS_DIR/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_map.mgh
>
> Does the order in the subject list file I specified in the --f flag above 
> need to be exactly the same as in the fsgd files I later used (below) to 
> compare the groups? If so, that might be the source of the problem. Here's my 
> mri_glmfit command:
>
> mri_glmfit --y 
> /$SUBJECTS_DIR/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_map.mgh 
> --fsgd /$SUBJECTS_DIR/fsgd/RPDR_083115/102PostFort_Minus_112PreFort.fsgd --C 
> /$SUBJECTS_DIR/fsgd/Top_Minus_Bottom.mtx --glmdir 
> /cluster/deplin/chris/data/Subjects/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_fwhm22
>  --surf fsaverage lh --fwhm 22 --no-prune
>
> Thanks!
> Hamdi
>
>
> 
> 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: Tuesday, November 03, 2015 2:34 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a 
> ROI
>
> The y.mgh file is created by your call to mris_preproc (or by a
> subsequent call to mri_surf2surf for smoothing). The order of the
> subjects depends on how you called mris_preproc (which should match that
> in the fsgd file or else everything will be bogus). The y.mgh file
> contains all the subjects in fsaverage space, so you don't need to run
> it for each subject or resample back into native space
>
> On 11/03/2015 02:29 PM, Eryilmaz, H. Hamdi wrote:
>> Hi Doug,
>>
>> Thanks for the reply. Sure I will try this command. But as it is now, how 
>> will mri_segstats know the order in the fsgd file? Also, this command needs 
>> to run for each subject, right? Then, which input file should I use for the 
>> --i flag?
>>
>> mri_segstats --slabel fsaverage lh contrast.fsaverage.label --i y.mgh--id 1 
>> --avgwf y.label.dat
>>
>>
>> Thanks a lot!
>> Hamdi
>>
>> 
>> 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: Tuesday, November 03, 2015 2:01 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a 
>> ROI
>>
>> On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
>>> Sorry, the figures I inserted in the text did not appear in the email.
>>> I attach them now.
>>>
>>> Best,
>>> Hamdi
>>>
>>> 
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eryilmaz, H.
>>> Hamdi [hamdi.eryil...@mgh.harvard.edu]
>>> *Sent:* Friday, October 30, 2015 1:32 PM
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* [Freesurfer] cortical thickness - comparing two groups
>>> within a ROI
>>>
>>> Dear FS experts,
>>>
>>> I have a question about extracting average cortical thickness from a
>>> manually created ROI. I am comparing 2 groups, namely PostFort and
>>> PreFort and my fsgd file appears as the following:
>>>
>>> GroupDescriptorFile 1
>>> Title PostPreFortification
>>> Class PostFort
>>> Class PreFort
>>>
>>> InputSubject1PostFort
>>> InputSubject2PostFort
>>> .
>>> .
>>> .
>>>
>>> The contrast that I use to compare these groups is [1 -1]. When I
>>> display the significance map for this contrast I get the following
>>> image on the left hemisphere:
>>>
>>>
>>>
>>>
>>> My first question is, those blue clusters represent regions, where
>>> thickness is greater in the PreFort group, don't they?
>> Correct
>>> Assuming this is correct, I created a label for this region (which
>>> contains about 3000 vertices) and extracted the thickness value from
>>> this region for each subject using the following commands. These
>>> commands are part of scripts in which $subject and $label are defined.
>>>
>>>
>>>
>>> _to make a label for each subject (the original label was created on
>>> fsaverage):_
>>> *mri_label2label* --srclabel $SUBJECTS_DIR/labels/${label}.label
>>> --srcsubject fsaverage --trglabel
>>> $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
>>> --regmethod surface --hemi lh
>>>
>>> _to create a stats file of this ROI containing several anatomical
>>> measures:_
>>> *mris_anatomical_stats* -f
>>> $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l
>>> $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh
>>>
>>> _to compile 

[Freesurfer] Freesurfer 6.0

[Hoptman, Matthew]

Hi all,
I can see a link for Freesurfer 6.0 on the website, but when I click on it to 
download, it just blinks at me.  I also tried to ftp to your ftp site, and 
unfortunately, I got the message
421 Proxy is closed (unknown user location).

Could you please tell me how I could get the new version of Freesurfer?
Thanks,
Matt
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended 
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Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

[Douglas N Greve]

When you ran mri_glmfit the first time, you had to specify a file with 
the --y flag. It is looking for that file now. Does that file still 
exist in the location where it was when you ran mri_glmfit?


On 11/03/2015 04:50 PM, s...@u.washington.edu wrote:
> Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in 
> [mydata}/cope7ACroi_rh.osgm.rfx.
>
> There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), 
> and even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, 
> gammavar, mask, and sig) but no rh.cope7.mgh.
>
> Thanks for going back and forth about this,
>
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> The correct command line is
>>
>> --cache 4 neg --cache-label AC
>>
>> On 11/03/2015 03:36 PM, s...@u.washington.edu wrote:
>>> Hi Doug,
>>>
>>>
>>>
>>> So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot
>>> find any documentation about what to put instead of --grf), as in
>>>
>>> mri_glmfit-sim --glmdir
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx
>>> --cache-label AC 4 neg --cwpvalthresh 0.05 --2spaces
>>>
>>> I get back "ERROR: Flag 4 is unrecognized."
>>>
>>> If I try just --cache instead of --cache-label AC, I get back "ERROR:
>>> cannot find
>>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/rh.cope7.mgh"
>>>
>>> Any thoughts?
>>>
>>> Many thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 The fwhm.dat file was in the right place. You passed the wrong folder to
 mri_glmfit-sim. You should pass it

 cope7ACroi_rh.osgm.rfx

 doug


 On 11/03/2015 02:40 PM, s...@u.washington.edu wrote:
> It's:
>
> mri_glmfit --y
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh
> --osgm --glmdir
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx
> --surf fsaverage lh --label
> /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label
>
> fwhm.dat is actually in [MyData]/cope7ACroi_rh.osgm.rfx rather than
> [MyData]/cope7ACroi_rh.osgm.rfx/osgm. I think that actually also
> happened for some other files needed and I moved them. Is the
> problem something in my mri_glmfit command?
>
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> it cannot find this file
>>
>> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat
>>
>>
>> which should have been created by mri_glmfit. What is your mri_glmfit
>> command line?
>>
>> Also, don't use --grf, that is for volumes only
>>
>>
>> On 11/03/2015 02:27 PM, s...@u.washington.edu wrote:
>>> Hi DOug,
>>>
>>> doug.log is attached
>>>
>>> the bash equivalent for |& is 2>&1 |
>>>
>>> thanks,
>>> Susan
>>>
>>> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>>>
 I meant &. The & works for tcsh (or csh). Are you using bash? I'm
 not
 sure what the bash equivalent is. Maybe |2 instead of |&
 perhaps some bash experts can weigh in

 On 11/03/2015 01:41 PM, s...@u.washington.edu wrote:
> Hi Doug,
>
> Do you mean:
>
>  mri_glmfit-sim --debug --glmdir
> /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm
>
> --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee
> doug.log?
>
> When I tried running the same code with |& tee doug.log at the end,
> I kept getting:
>
> syntax error near unexpected token `&'
>
> Thanks,
> Susan
>
> On Tue, 3 Nov 2015, Douglas N Greve wrote:
>
>> Can you run
>>
>> mri_glmfit-sim --debug --glmdir [my data
>> dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg
>> --cwpvalthresh 0.05 --2space |& tee doug.log
>>
>> and send me doug.log?
>>
>>
>>
>>
>> On 11/02/2015 05:08 PM, s...@u.washington.edu wrote:
>>> Hi experts,
>>>
>>> I am having trouble performing a Monte Carlo correction using
>>> mri_glmfit-sim.
>>>
>>> My data were sampled to fsaverage and smoothed at fwhm 5, using
>>> mris_preproc. I then ran mri_glmfit on the data.
>>>
>>> I want to do my analysis/correction only in auditory cortex (AC)
>>> so I did my own simulation in AC of each hemisphere using
>>> mri_mcsim (as per
>>> http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo).
>>>
>>> So far, so good.
>>>
>>> But when I try to run:
>>>
>>> mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm
>>> --cache-label AC --grf 4 

[Freesurfer] preproc-sess and stc question

[Gay,Charles Wysaw]

Hi -

1) I am trying to perform preprocessing steps on functional task data that was 
acquired on a Phillips scanner using an interleaved acquisition. There are 42 
slices and the order is 
[0,6,12,18,24,30,36,1,7,13,19,25,31,37,2,8,14,20,26,32,38,3,9,15,21,27,33,39,4,10,16,22,28,34,40,5,11,17,23,29,35,41].
 I've tried
 -slice order followed by the sequence but that didn't seem to work. And I 
wasn't able to find anything in stc-sess -help that explained how to enter the 
exact sequence order.
If you could show me how to add/change the tutorial code below, that would be 
great. Thanks.
2) Do I need to modify the onsets in the paradigmfile?

Thanks,
Chaz



preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 
5 -per-run
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Re: [Freesurfer] unit in 'search area' in the glmfit log

[Jeni Chen]

Thank you Doug. I was actually referring to the following values (example of my 
log output below):

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /Volumes/pathname
cmdline mri_glmfit --y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh --C 
./pathname/tmp.mri_glmfit-sim-34418/Group-diff_abcd.mtx --C 
./pathname/tmp.mri_glmfit-sim-34418/Group-avg_abcd.mtx --mask 
./pathname/mask.mgh --sim mc-z 5000 1.3 ./pathname/csd/mc-z.abs.1.3.j001 
--sim-sign abs --fwhm 13.034857 --fsgd ./pathname/y.fsgd dods --label 
/Volumes/pathname/lh_abcd_mask.label --surf fsaverage lh white 
sysname  Darwin
hostname computer.local
machine  x86_64
user jeni
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
fwhm 13.034857
niters125.00
OneSampleGroupMean 0
y/Volumes/pathname/lh.Group_abcd.thickness.10.mgh
logyflag 0
usedti  0
FSGD ./pathname/y.fsgd
labelmask  /Volumes/pathname/lh_abcd_mask.label
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from /Volumes/pathname/lh.Group_abcd.thickness.10.mgh
INFO: gd2mtx_method is dods
Normalized matrix condition is 14.1782
Matrix condition is 289425
Found 9260 points in label.
Found 7440 voxels in mask
Reshaping mriglm->mask...
search space = 3795.353314
DOF = 37
thresh = 1.3, threshadj = 0.99897 

I do see that it gives information on the number of voxels in the mask (which 
is 7440 in the above example). What I was referring to is the next number 
"search space = 3795.35..."
Is that the search area?

Also in your reply, I see the need to specify the mask.mgh. How do I specify it 
if my mask is a label file and not in mgh format?

Thanks again.

Jeni

> On Fri, 30 Oct 2015 08:21 PM Douglas Greve wrote:
> That number is in voxels or vertices. If you want surface area, then use 
> mri_segstats something like
>> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh 
>> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat
>> 
>> doug
>> 
>> On 10/29/15 5:10 PM, Jeni Chen wrote:
>> > Hello,
>> >
>> > When running the Clusterwise Correction for Multiple Comparisons, I used a 
>> > label as a mask to restrict search area. I want to find out the size of 
>> > that 
>> > label, so I guess I can pull that information out from the 
>> > "mri_glmfit.log", 
>> > specifically under 'searchspace'? Also I only see a numerical value there, 
>> > I 
>> > assume it is in mm2?
>> >
>> > Thanks.
>> >
>> > Jeni

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Re: [Freesurfer] unit in 'search area' in the glmfit log

[Douglas N Greve]

On 11/03/2015 07:03 PM, Jeni Chen wrote:
> Thank you Doug. I was actually referring to the following values 
> (example of my log output below):
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /Volumes/pathname
> cmdline mri_glmfit --y 
> /Volumes/pathname/lh.Group_abcd.thickness.10.mgh --C 
> ./pathname/tmp.mri_glmfit-sim-34418/Group-diff_abcd.mtx --C 
> ./pathname/tmp.mri_glmfit-sim-34418/Group-avg_abcd.mtx --mask 
> ./pathname/mask.mgh --sim mc-z 5000 1.3 
> ./pathname/csd/mc-z.abs.1.3.j001 --sim-sign abs --fwhm 13.034857 
> --fsgd ./pathname/y.fsgd dods --label 
> /Volumes/pathname/lh_abcd_mask.label --surf fsaverage lh white
> sysname  Darwin
> hostname computer.local
> machine  x86_64
> user jeni
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> fwhm 13.034857
> niters  125.00
> OneSampleGroupMean 0
> y  /Volumes/pathname/lh.Group_abcd.thickness.10.mgh
> logyflag 0
> usedti  0
> FSGD ./pathname/y.fsgd
> labelmask  /Volumes/pathname/lh_abcd_mask.label
> maskinv 0
> glmdir (null)
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Loading y from /Volumes/pathname/lh.Group_abcd.thickness.10.mgh
> INFO: gd2mtx_method is dods
> Normalized matrix condition is 14.1782
> Matrix condition is 289425
> Found 9260 points in label.
> *Found 7440 voxels in mask*
> *Reshaping mriglm->mask...*
> *search space = 3795.353314*
> DOF = 37
> thresh = 1.3, threshadj = 0.99897
>
> I do see that it gives information on the number of voxels in the mask 
> (which is 7440 in the above example). What I was referring to is the 
> next number "search space = 3795.35..."
> Is that the search area?
Yes, that is the surface area of the search space. The mri_segstats 
command should give you the same value as above. If you want to run it, 
use the mask.mgh that gets created when mri_glmfit is run
>
> Also in your reply, I see the need to specify the mask.mgh. How do I 
> specify it if my mask is a label file and not in mgh format?
>
> Thanks again.
>
> Jeni
>
>> On Fri, 30 Oct 2015 08:21 PM Douglas Greve wrote:
>> That number is in voxels or vertices. If you want surface area, then use
>> mri_segstats something like
>>> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh 
>>> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat doug On 
>>> 10/29/15 5:10 PM, Jeni Chen wrote: > Hello, > > When running the 
>>> Clusterwise Correction for Multiple Comparisons, I used a > label as 
>>> a mask to restrict search area. I want to find out the size of that 
>>> > label, so I guess I can pull that information out from the 
>>> "mri_glmfit.log", > specifically under 'searchspace'? Also I only 
>>> see a numerical value there, I > assume it is in mm2? > > Thanks. > 
>>> > Jeni
>

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

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

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[Freesurfer] 1.5T vs 3.0T longitudinal study...

[Gonzalo Rojas Costa]

Hi:

I have two timepoints of the same patient: the first is in 1.5T and the
second in 3.0T... Is it possible to do the longitudinal study (subcortical
volumes) using the Workflow Summary described in
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ?...

Sincerely,

Gonzalo Rojas Costa

-- 
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clinica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
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Re: [Freesurfer] 1.5T vs 3.0T longitudinal study...

[Martin Reuter]

Hi Gonzalo,

it is possible to run those tools on that data. The problem is you will 
never know if the effect you find is due to anatomical changes or 
scanner / field strength differences. Maybe you could scan 10-20 
controls on the 1.5 and 3 T scanner back to back , to estimate scanner 
effects (using the assumption that anatomical changes are close to zero, 
which of course could be wrong, as there will be motion and hydration 
effects. Both could be affected by the order of scans, so I would 
randomly select which scan is done first (1.5 or 3T). Anyway with that 
data you could compare your effect with the test-retest scanner effect 
to see if there are significant differences.


Best, Martin

On 11/03/2015 07:41 PM, Gonzalo Rojas Costa wrote:


Hi:

I have two timepoints of the same patient: the first is in 1.5T and 
the second in 3.0T... Is it possible to do the longitudinal study 
(subcortical volumes) using the Workflow Summary described in 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ?...


Sincerely,

Gonzalo Rojas Costa

--
Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel:56-9-97771785 
www.clc.cl 


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clinica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile
Tel: 56-2-2105170
Cel:56-9-97771785 
www.clc.cl 



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--
Martin Reuter, PhD
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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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

[Martin Reuter]

Hi Pablo,

setting up that matrix is designing your model. You would probably add 
the 2 columns (1x5 and 2x5) to your matrix. Having independent matrices 
for each group, is a different model (actually 2 different ones).


Best, Martin

On 11/03/2015 04:33 PM, pablo najt wrote:

Thank you Martin.
My intention was not to enquire about advice on the statistical model 
but instead on how to run the matlab commad with two experimental groups.
My decision is to test group by age interaction for each group. The 
way to proceed for this would be to create two separate matrices?

Thanks
Pablo


To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Tue, 3 Nov 2015 12:10:17 -0500
Subject: Re: [Freesurfer] A mixed effect model approach in within 
subject dataset {Disarmed}


Dear Pablo,
maybe what you want is a group x age interaction for each of those 
groups? (so 1x5 and 2x5)?
Not sure. It is your hypothesis, your model and we usually don't give 
advise on model building. Since you have a special case (within family 
analysis) I would recommend you try to get some advise from a 
bio-statistician, if unsure what you are doing.


Best, Martin


On 11/03/2015 12:01 PM, pablo najt wrote:

Dear Martin and FS experts.
I have a quick query about how to obtain my design matrix of
/group by age/ from the following matlab command listed in the lme
wiki. In the wiki example the matrix is created from variables 1
and 2 (group by time).

 X = [ones(length(M),1) M M(:,1).*M(:,2);

In my case I have a combination of variables 1 and 2 for group
(relatives of PT and PT) and 5 (age).
I would really appreciate if you could kindly advice on how to
adapt the command above to my design.
Thanks
Pablo


To: freesurfer@nmr.mgh.harvard.edu

From: mreu...@nmr.mgh.harvard.edu 
Date: Tue, 27 Oct 2015 17:13:51 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within
subject dataset {Disarmed}

Hi Pablo,

the sortData function sorts the rows so that entries from the same
subject (in your case same family) are blocked and that within
each block the time variable (2nd parameter specifies which column
that is in your M matrix, in your case the first =1) is increasing.
It is important, when creating your design matrix X, that ordering
agrees with Y. That is guaranteed if you generate X from M (which
is ordered like Y after the sort command).

Best, Martin

On 10/27/2015 01:32 PM, pablo najt wrote:

Thank you for your input.
I noticed that if I follow literally all the steps in the
wiki, my data which is ordered by variable 'family' (instead
of subjects, in my case is number of members belonging to e.g.
family_1) is shuffled. This happens after I run the command
sortData below. Especially I noticed that ni and X do not
match sID.
It would be really helpful to know what is this command doing.
I am wondering whether my data differs in number of columns or
else and because of this I end with a shuffled data. Any
suggestion or tips to figure what could be happening?
Thanks
Pablo

[M, Y, ni] = sortData(M,1,Y,sID)


To: freesurfer@nmr.mgh.harvard.edu

From: mreu...@nmr.mgh.harvard.edu

Date: Wed, 14 Oct 2015 10:54:41 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in
within subject dataset {Disarmed}

Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)

see
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels


hope that helps, Martin


On 10/14/2015 10:43 AM, pablo najt wrote:

Dear FS experts.
I have query about a relating to a previous email
(below). I am aiming to run a LME analysis on
cross-sectional data from different families and have
variable 'family' (number of families) as my NI vector.
My design has three groups and therefore I am not able to
use qdec. I am running the matlab commands below and
finding some difficulty would really appreciate if you
could help out.
Thanks
Pablo

Start analysis as follows:

1-Read your label eg.:
lhcortex =

fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data 

Re: [Freesurfer] unit in 'search area' in the glmfit log

[Chen Jen-I.]

> On Nov 3, 2015, at 8:01 PM, Douglas N Greve  wrote:
> 
>> Found 9260 points in label.
>> *Found 7440 voxels in mask*
>> *Reshaping mriglm->mask...*
>> *search space = 3795.
>> 
>> I do see that it gives information on the number of voxels in the mask 
>> (which is 7440 in the above example). What I was referring to is the next 
>> number "search space = 3795.35..."
>> Is that the search area?
> Yes, that is the surface area of the search space. The mri_segstats command 
> should give you the same value as above. If you want to run it, use the 
> mask.mgh that gets created when mri_glmfit is run

Thanks! And that's in mm^2, correct?

Jeni 
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Re: [Freesurfer] unit in 'search area' in the glmfit log

[Douglas Greve]

yes, mm2

On 11/3/15 9:06 PM, Chen Jen-I. wrote:
>> On Nov 3, 2015, at 8:01 PM, Douglas N Greve  
>> wrote:
>>
>>> Found 9260 points in label.
>>> *Found 7440 voxels in mask*
>>> *Reshaping mriglm->mask...*
>>> *search space = 3795.
>>>
>>> I do see that it gives information on the number of voxels in the mask 
>>> (which is 7440 in the above example). What I was referring to is the next 
>>> number "search space = 3795.35..."
>>> Is that the search area?
>> Yes, that is the surface area of the search space. The mri_segstats command 
>> should give you the same value as above. If you want to run it, use the 
>> mask.mgh that gets created when mri_glmfit is run
> Thanks! And that's in mm^2, correct?
>
> Jeni
>
>

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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Clara Kühn]

With the FS 6 beta version the problem doesn't occur.
Cheers, Clara

- Ursprüngliche Mail -
Von: "Ruopeng Wang" 
An: "Freesurfer support list" 
Gesendet: Dienstag, 3. November 2015 18:03:52
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Try 6.0.0beta.

On 11/03/2015 12:02 PM, Clara Kühn wrote:
> Our IT guy said it could be a software problem since he didn't have the 
> problem and the only difference between out computers was the display.
> We have these versions at the institute:
>
> 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
> Is the first one the dev version?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Ruopeng Wang" 
> An: "Freesurfer support list" 
> Gesendet: Dienstag, 3. November 2015 17:57:50
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> There was a bug in freeview in FS 5.3.0 that may have caused the crash. 
> Clara, can you try the dev version of freeview?
>
> Ruopeng
>
> On 11/03/2015 11:50 AM, Bruce Fischl wrote:
>
>
> Hi Clara
>
> that doesn't crash for me. Are you sure you ahve write permission to the 
> file? And that the disk isn't full? Ruopeng: any other ideas?
>
> Bruce
>
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Hi Bruce,
>
> I attached the wm.mgz from one of my participants. It happens with any 
> participant though.
> What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and 
> then it crashes with afore mentioned error message.
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Bruce Fischl" 
> An: "Freesurfer support list" 
> Gesendet: Dienstag, 3. November 2015 14:42:25
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> Hi Clara
>
> can you send us the wm.mgz and tell us exactly what you did to make it
> crash?
>
> thahks
> Bruce
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Dear FreeSurfer experts,
>
> since last week I have the problem that FS (5.3.0) crashes when I try to save 
> changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
> always restore it by renaming the temporary file (wm.mgz~) but it obviously 
> doen't save any changes.
>
> I've tried different computers (same FS version) and on some it works and on 
> some the same problem occurs. I just tried it on the 6.0.0beta version and it 
> saved like a charm. I would rather, however, keep editing my data with the 
> same version.
> Here is the error message I get in the terminal:
>
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal
>  [0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on 
> Apple to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
> 17:22:55 2015
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> Segmentation fault (core dumped)
>
> Any idea what it means by Segmentation Violation and how I can fix it??
> Cheers and thanks in advance!
> Clara Kühn
>
> ___
> 

Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

[Razlighi, Qolamreza R.]

Thanks Bruce,
I read in another post that these coordinates in ascii file are in native 
space. So if I load the original volume in another visualization tool (e.g. 
fslview), these coordinates should be right on the border of white/gray matter. 
Is that correct?
I already checked couple of them but wanted to be sure this is the case.
Also, if freeview doesn’t get the header information from ascii files, what 
header info (probably a default one) it uses to plot them? Is there any way we 
can give those header information separately to freeview?

Best

--
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University

Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/

On Nov 2, 2015, at 10:02 AM, Bruce Fischl 
> wrote:

Hi Ray

the ascii format is pretty barebones and doesn't have e.g. ras2vox info
that freeview uses to display the surfaces properly.  It's for ease of
conversion and such.

cheers
Bruce

On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote:

Hi Guys,
Why converting a surface to .asc format changes its spatial orientation? 
Specifically, I have converted lh.while to lh.white.asc (using: mris_convert 
lh.white lh.white.asc) and plot both of them using freeview but they are not 
corresponding. In fact, lh.white corresponds to the volume image (e.g orig.mgz) 
but the lh.white.asc doesn't. See the attached screenshot. The red curve is the 
lh.white.asc.
Any explanation would be greatly appreciated.

Best


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[Freesurfer] Freesurfer crash upon wm.mgz changes

[Clara Kühn]

Dear FreeSurfer experts,

since last week I have the problem that FS (5.3.0) crashes when I try to save 
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
always restore it by renaming the temporary file (wm.mgz~) but it obviously 
doen't save any changes.

I've tried different computers (same FS version) and on some it works and on 
some the same problem occurs. I just tried it on the 6.0.0beta version and it 
saved like a charm. I would rather, however, keep editing my data with the same 
version. 
Here is the error message I get in the terminal:

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
17:22:55 2015
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn

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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Bruce Fischl]

Hi Clara

can you send us the wm.mgz and tell us exactly what you did to make it 
crash?


thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:


Dear FreeSurfer experts,

since last week I have the problem that FS (5.3.0) crashes when I try to save 
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
always restore it by renaming the temporary file (wm.mgz~) but it obviously 
doen't save any changes.

I've tried different computers (same FS version) and on some it works and on 
some the same problem occurs. I just tried it on the 6.0.0beta version and it 
saved like a charm. I would rather, however, keep editing my data with the same 
version.
Here is the error message I get in the terminal:

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
17:22:55 2015
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn

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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Bruce Fischl]

Hi Clara

that doesn't crash for me. Are you sure you ahve write permission to the 
file? And that the disk isn't full? Ruopeng: any other ideas?


Bruce

On Tue, 3 Nov 2015, Clara Kühn wrote:


Hi Bruce,

I attached the wm.mgz from one of my participants. It happens with any 
participant though.
What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then 
it crashes with afore mentioned error message.

Cheers, Clara

- Ursprüngliche Mail -
Von: "Bruce Fischl" 
An: "Freesurfer support list" 
Gesendet: Dienstag, 3. November 2015 14:42:25
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Hi Clara

can you send us the wm.mgz and tell us exactly what you did to make it
crash?

thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:


Dear FreeSurfer experts,

since last week I have the problem that FS (5.3.0) crashes when I try to save 
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
always restore it by renaming the temporary file (wm.mgz~) but it obviously 
doen't save any changes.

I've tried different computers (same FS version) and on some it works and on 
some the same problem occurs. I just tried it on the 6.0.0beta version and it 
saved like a charm. I would rather, however, keep editing my data with the same 
version.
Here is the error message I get in the terminal:

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
17:22:55 2015
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn

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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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