[Freesurfer] Changing operating system.

[Ramesh Babu]

Dear Experts,

Recently I am facing lot of problem with Ubuntu OS 16lts. In one year I
have formatted 4 times because of nvidia graphic card driver issue (happens
after update) or some unknown reason ( I am not tech tech guy to figure out
all the problem). Yesterday onwards problem started again. I couldn't open
ubuntu. Initially it was blank screen, after following some suggestion from
forum I removed nvidia driver and tried lot other things. Still not
functioning. Therefore I am planning to go for cent os.

After installing cent os should I redo all analysis again? or I can
continue with whatever so far done by using Ubuntu os?

Thanks
RB
___
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] Destrieux (aparc2009) atlas in MNI 2mm space?

[Daya P]

Hi All,

How can I get the aparc2009 atlas in MNI 2mm space? I want the labels to be
in MNI 2mm space. Are there Destrieux labels in 2mm space already
somewhere? I could only find them in 1mm ...

Thank you,
Daiana
___
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.

Re: [Freesurfer] QDEC

[Kinzel, Phillipp]

Hi Doug, l figured it out: I had moved the project file and the qdec.table.dat 
files to other directories which is why qdec couldn´t retrieve them!

Thanks, Philipp

Von:  im Auftrag von Douglas Greve 

Antworten an: Freesurfer support list 
Datum: Freitag, 10. November 2017 um 14:31
An: "freesurfer@nmr.mgh.harvard.edu" 
Betreff: Re: [Freesurfer] QDEC


No idea. Can you send the file?

On 11/9/17 12:42 PM, Kinzel, Phillipp wrote:
Hi Doug,

do you have any other ideas why I can´t open the project file?

Best, Philipp

Von: 

 im Auftrag von "Kinzel, Phillipp" 

Antworten an: Freesurfer support list 

Datum: Mittwoch, 8. November 2017 um 14:33
An: Freesurfer support list 

Betreff: Re: [Freesurfer] QDEC

Hi Douglas, thank you for your quick response. Yes, I have permission to read 
and write for the file. I modified the permission to be able to execute the 
file as well, but that didn´t change anything. I created the file through the 
qdec- GUI and didn´t have any problems while running the GLM.

Von: 

 im Auftrag von Douglas Greve 

Antworten an: Freesurfer support list 

Datum: Mittwoch, 8. November 2017 um 09:51
An: "freesurfer@nmr.mgh.harvard.edu" 

Betreff: Re: [Freesurfer] QDEC


Do you have permission to read it? How was it created?

On 11/8/17 1:18 AM, Kinzel, Phillipp wrote:
Hi, I have problems loading project  files in QDEC.

I get the following error:

Loading data table /tmp/qdec_project_archive/qdec.table.dat...
ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
Error loading the project file.

I would be greatful for any advice.

Best, Philipp








___

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


___
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.

Re: [Freesurfer] dt_recon and Tracula

[Mehta, Chintan]

Dear Doug,

I figured out the mistake I was making, which was that I ran:


> freeview -v orig.mgz wmparc2diff.mgz:colormap=lut 
> lowb.nii.gz:reg=register.dat -f lh.white:edgecolor=green 
> rh.white:edgecolor=green -viewport coronal &

Here the lowb, orig, and white surfaces were consistent. Since wmparc2diff.mgz 
is in diffusion space, it was bound to be mismatched with the lowb & white 
surface lines. When replacing wmparc2diff.mgz with wmparc.mgz, it is no 
surprise that there is a much better match between the white matter 
parcellation & lowb.

There is a very good match between lowb and wmparc2diff, when running, per the 
documentaiton,
> freeview -v lowb.nii.gz wmparc2diff.mgz:colormap=lut -f 
> lh.white:edgecolor=green rh.white:edgecolor=green -viewport coronal &

However, the lh.white and rh.white surfaces do not change. I suppose this is 
because those surfaces are not for volumes registered to the diffusion space. 
Does that make sense? Or would the lh.white and rh.white automatically adjust 
to diffusion space?

Thank you.

Best,
Chintan




___
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] Flux Satellite Conference

[Margaret Sheridan]

*UNC Chapel Hill, in association with The Flux Society, *will host a
conference highlighting research using large, representative, or publicly
available datasets to investigate developmental cognitive neuroscience.
This conference will address the unique ability of larger, more
representative datasets–and particularly those with multiple time points–to
ask questions about brain development that have historically been
impossible to address with the smaller, cross-sectional samples utilized in
most neuroimaging research studies. The focus will be on research
leveraging large datasets to understand functional and structural brain
development in the context of connectomics, environmental influences on
brain development, and typical and atypical trajectories of brain
development.

The conference will take place at UNC Chapel Hill May 6 – May 8, 2018.

Abstract submission deadline: 1/22/18
Registration opens: 2/1/18

For more information and to submit your abstract, visit:
http://fluxsatellite.web.unc.edu/

You may also sign up for the conference listserv on the site to receive
future announcements.
___
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.

Re: [Freesurfer] hemisphere analysis

[Douglas Greve]

Yes


On 11/10/17 2:45 PM, lanbo Wang wrote:

Thank you very much, it's work.
I have another question, this is for structural imaging. Can I use 
those steps for fmri or DTI imaging?


On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve 
> wrote:


Don't use --conjunct, just mri_concat file1 file2 ... file N --o
output


On 11/10/17 12:56 PM, lanbo Wang wrote:

I firstly did mris_preproc separately. Secondly used fscalc to
reverse left symptom subjects. Thirdly used mri_concat --conjunct
to combine all the subjects together.

The code is:
1.mris_preproc --target fsaverage_sym --hemi lh \
  --xhemi --paired-diff \
  --srcsurfreg fsaverage_sym.sphere.reg \
  --meas thickness \
  --out lh.lh-rh.thickness.sm00.s02.mgh \
  --s subj_02_1
2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o
lh.lh-rh.thickness.sm00.s09.mgh
3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh
lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh
lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh
lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh
lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh
lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh
lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh
lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh
lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh
lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh
lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh
lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh
lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh
lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh
4.smooth
5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh


On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve
> wrote:

Do you only have one subject in your input file? You need to
run mris_preproc separately for each subject, create a
different file for each, then mri_concat the files together


On 11/9/17 6:20 PM, lanbo Wang wrote:

Dr. Douglas,

I try #3 method, when I run mri_glmfit, get error.
The code I used:
[mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y
lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
Reading source surface
/HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area 61972.710938
AvgVtxArea   0.378247
AvgVtxDist   0.693419
StdVtxDist   0.190498

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user mtobia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
ickness.sm10.mgh
logyflag 0
usedti  0
labelmask
/HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label
maskinv 0
glmdir glm.lh.lh-rh.thickness.sm10
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory glm.lh.lh-rh.thickness.sm10
Loading y from
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
ickness.sm10.mgh
Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 146902 points in label.
Pruning voxels by thr: 0.00
Found 146902 voxels in mask
Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
Reshaping mriglm->mask...
search space = 79288.081914
DOF = 0
ERROR: DOF = 0

The code I used before this one is
How can I resolve this problem.

Thanks,
Lanbo


On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve
> wrote:

which code. I gave 3 options below, which one did you use?


On 11/07/2017 02:43 PM, lanbo Wang wrote:
> I try to use this code to compare left and right
hemisphere by paired
> t-test  and add age as covariate.
>
  

Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

Thank you very much, it's work.
I have another question, this is for structural imaging. Can I use those
steps for fmri or DTI imaging?

On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve 
wrote:

> Don't use --conjunct, just mri_concat file1 file2 ... file N --o output
>
> On 11/10/17 12:56 PM, lanbo Wang wrote:
>
> I firstly did mris_preproc separately. Secondly used fscalc to reverse
> left symptom subjects. Thirdly used mri_concat --conjunct to combine all
> the subjects together.
>
> The code is:
> 1.mris_preproc --target fsaverage_sym --hemi lh \
>   --xhemi --paired-diff \
>   --srcsurfreg fsaverage_sym.sphere.reg \
>   --meas thickness \
>   --out lh.lh-rh.thickness.sm00.s02.mgh \
>   --s subj_02_1
> 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o
> lh.lh-rh.thickness.sm00.s09.mgh
> 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh
> lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh
> lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh
> lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh
> lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh
> lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh
> lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh
> lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh
> lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh
> lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh
> lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh
> lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh
> lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh
> lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh
> 4.smooth
> 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
> glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
>
>
> On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve  > wrote:
>
>> Do you only have one subject in your input file? You need to run
>> mris_preproc separately for each subject, create a different file for each,
>> then mri_concat the files together
>>
>> On 11/9/17 6:20 PM, lanbo Wang wrote:
>>
>> Dr. Douglas,
>>
>> I try #3 method, when I run mri_glmfit, get error.
>> The code I used:
>> [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y
>> lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm
>> --surf fsaverage_sym lh
>> Reading source surface /HD4/subjects_results_symptom/
>> /fsaverage_sym/surf/lh.white
>> Number of vertices 163842
>> Number of faces327680
>> Total area 61972.710938
>> AvgVtxArea   0.378247
>> AvgVtxDist   0.693419
>> StdVtxDist   0.190498
>>
>> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>> cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
>> cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
>> glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
>> sysname  Linux
>> hostname localhost.localdomain
>> machine  x86_64
>> user mtobia
>> FixVertexAreaFlag = 1
>> UseMaskWithSmoothing 1
>> OneSampleGroupMean 1
>> y/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
>> ickness.sm10.mgh
>> logyflag 0
>> usedti  0
>> labelmask  /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex
>> .label
>> maskinv 0
>> glmdir glm.lh.lh-rh.thickness.sm10
>> IllCondOK 0
>> ReScaleX 1
>> DoFFx 0
>> Creating output directory glm.lh.lh-rh.thickness.sm10
>> Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/
>> lh.lh-rh.thickness.sm10.mgh
>> Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
>> Normalized matrix condition is 1
>> Matrix condition is 1
>> Found 146902 points in label.
>> Pruning voxels by thr: 0.00
>> Found 146902 voxels in mask
>> Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
>> Reshaping mriglm->mask...
>> search space = 79288.081914
>> DOF = 0
>> ERROR: DOF = 0
>>
>> The code I used before this one is
>> How can I resolve this problem.
>>
>> Thanks,
>> Lanbo
>>
>>
>> On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> which code. I gave 3 options below, which one did you use?
>>>
>>>
>>> On 11/07/2017 02:43 PM, lanbo Wang wrote:
>>> > I try to use this code to compare left and right hemisphere by paired
>>> > t-test  and add age as covariate.
>>> >
>>> > Thanks,
>>> > Lanbo
>>> >
>>> > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
>>> > > wrote:
>>> >
>>> > which method are you trying to implement? If #3, then you need to
>>> run
>>> > mris_preproc separately for each subject, and then run that fscalc
>>> > command
>>> >
>>> >
>>> > On 11/07/2017 11:33 AM, lanbo Wang wrote:
>>> > > Hi Douglas,
>>> > >
>>> > > Thanks for your reply.
>>> > > I created the fsgd file as you show me, and run code like this.
>>> Am I
>>> > > right?
>>> > > 1.
>>> > 

Re: [Freesurfer] Trans. : VBM question

[Douglas Greve]

No, sorry. You can always use the command line stream (mris_preproc, 
mri_surf2surf, create your fsgd file with your covariates of interest, 
and then run mri_glmfit)


On 11/10/17 4:13 AM, m.ba...@uliege.be wrote:
> Dear Douglas,
>
> Thank you very much for you answer. I checked all the aparc stat files 
> (/Freesurfer/subjects/subjectID/stats/lh.aparc.stats; lh.aparc.a2009s.stats 
> ) and my region of interest "perirhinal" (region extending on BA35 and 
> BA36 areas) is only present on the lh/rh.BA.stats files 
> (/Freesurfer/subjects/subjectID/stats/lh.BA.stats and rh.BA.stats). I use 
> Freesurfer version 5.3. When using Qdec tool the only uploadable files are 
> .aparc files. Is it possible to upload also the regions of BA.stats files?
>
> Best regards,
> Mohamed
>
> - Mail original -
> De: "Douglas N Greve" 
> À: "Mohamed Ali Bahri" , freesurfer@nmr.mgh.harvard.edu
> Envoyé: Lundi 6 Novembre 2017 23:44:43
> Objet: Re: [Freesurfer] Trans. : VBM question
>
> Hi Mohamed, please remember to post to the list. As for your question,
> what aparc files are you looking at? Those measures are in, eg,
> lh.aparc.stats
>
>
> On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote:
>> Dear Douglas,
>>
>> Many thanks for your answer!
>>
>> We are interested on one region belonging to the Brodmann areas
>> "Perirhinal". Cortical thickness as well as volume values appear on
>> the BA stat list and not on the aparc or aseg lists. Does the
>> ROI-based analysis could be used for this BA region?
>>
>> Best regards,
>>
>> Mohamed
>>
>>
>> On 05/11/2017 18:46, Douglas Greve wrote:
>>> Do you just want to do an ROI analysis? Or do you want to do a
>>> voxel-based analysis? If ROI-based, then follow the steps on the ROI
>>> tutorial (ie, aparcstats2table and mri_glmfit with --table input).
>>>
>>>
>>> On 11/3/17 4:08 PM, Bruce Fischl wrote:
 Hi Mohamed

 Doug is away this week and can give you a more details answer next
 week. Certainly you could use mris_anatomical_stats -l >>> file name> to compute the volume/thickness/area for each subject
 then do whatever GLM analysis you want outside of FS.

 cheers
 Bruce


   On Fri, 3 Nov 2017, m.ba...@uliege.be wrote:

> Dear All,
> Does anyone have an answer to the following VBM question?
>
> Many thanks in advance,
> Regards
>
> -Mail original-
> De: "Mohamed Ali Bahri" 
> À: "Freesurfer support list" 
> Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM
> Objet: [Freesurfer] VBM question
>
> Dear Freesurfer users,
>
> I would like to study the between groups changes of volume/cortical
> thickness of one region (Perirhinal) belonging to the Brodmann
> areas. I
> tried to do that with Qdec tool but unfortunately Qdec does not
> load the
> Brodmann areas stat list. I am wondering if I could use the GLM
> formalism with of course regressing out the ITV. Any suggestion/advice
> will be very welcome.
>
> Many thanks in advance,
>
> Best regards,
>
> Mohamed
>
>

 ___
 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
>>>
>>>
>>> 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.
>> -- 
>> Dr. Mohamed Ali Bahri,
>> 1er Logisticien de Recherche,
>> Cyclotron Research Centre,
>> University of Liège, Belgium
>> m.ba...@uliege.be

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

Re: [Freesurfer] Optseq and de convolution for rapid designs

[fmri2013]

Many thanks Douglas  
If I optimise my design using Optseq, do you know if this de convolution 
process is implemented in SPM or any other software? and it is part of the 
processing behind th3 scenes?  Or do I have to account for this using a 
specific software. 
Aser


Sent from my Samsung Galaxy smartphone.
 Original message From: Douglas Greve 
 Date: 10/11/2017  19:24  (GMT+00:00) To: 
freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq and de 
convolution for rapid designs 

It is because the random jitter creates differential amounts of
  overlap. Imagine if you have A=C+D and B=C-D. You know A and B,
  but you want C and D. You have two equations and two unknowns, so
  you can solve for C and D from A and B eventhough C and D
  "overlap" in A and B and you never see C or D by themselves. This
  is a type of deconvolution




On 11/10/17 11:38 AM, Aser A wrote:



  
Hi all



I used Optseq
   to optimize rapid event designs with multiple conditions . I
  have a theortical question : how it is possible to distingwoh
  the close by trials ? Is it by de convoution ? How is it
  possible to deal with overallped trials ? 



Is it because the
  conditions are random so that when averaging them the distingwoh is
  possible?



Many thanks 



Aser



  
  

  
  

  ___
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


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] QDEC

[Douglas Greve]

No idea. Can you send the file?


On 11/9/17 12:42 PM, Kinzel, Phillipp wrote:


Hi Doug,

do you have any other ideas why I can´t open the project file?

Best, Philipp

*Von: * im Auftrag von 
"Kinzel, Phillipp" 

*Antworten an: *Freesurfer support list 
*Datum: *Mittwoch, 8. November 2017 um 14:33
*An: *Freesurfer support list 
*Betreff: *Re: [Freesurfer] QDEC

Hi Douglas, thank you for your quick response. Yes, I have permission 
to read and write for the file. I modified the permission to be able 
to execute the file as well, but that didn´t change anything. I 
created the file through the qdec- GUI and didn´t have any problems 
while running the GLM.


*Von: * im Auftrag von Douglas 
Greve 

*Antworten an: *Freesurfer support list 
*Datum: *Mittwoch, 8. November 2017 um 09:51
*An: *"freesurfer@nmr.mgh.harvard.edu" 
*Betreff: *Re: [Freesurfer] QDEC

Do you have permission to read it? How was it created?

On 11/8/17 1:18 AM, Kinzel, Phillipp wrote:

Hi, I have problems loading project  files in QDEC.

I get the following error:

Loading data table /tmp/qdec_project_archive/qdec.table.dat...

ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat

Error loading the project file.

I would be greatful for any advice.

Best, Philipp





___

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


___
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.

Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Douglas Greve]

It looks like it is a scripting problem where you did not include a 
backslash to indicate that the command line continued to the next line 
and so it thinks that "-=-iv" is a command (I assume that "commande 
introuvable" means something like "command  not found")



On 11/9/17 12:39 PM, Elisa Castaldi wrote:

Thank you very much for your help,
that almost fixed the problem.. Indeed it seems like it worked well 
for the first subject, but then it crashed for the second one..

this is the last part of what it typed on the command window:

%
Cleaning up
---
rm -r ./tmp.mris_preproc.2277
mardi 7 novembre 2017, 17:12:21 (UTC+0100)
mris_preproc done
SUBJECTS_DIR$ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii 
${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat\

> --projfrac 0.5 \
>
--iv : commande introuvable


For the first subject it correctly created the lh.con.mris_preproc.log 
file

Any idea?
Thanks


On 7 November 2017 at 17:00, Douglas N Greve 
> wrote:


looks like you did not create the lta file properly. You can just pass
mris_preproc the .dat file instead of the lta.


On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
> Yes, the output is in native functional space.
>
> On 7 November 2017 at 16:40, Douglas N Greve
> 
>> wrote:
>
>     Did you keep the spm output in native functional space?
>
>
>     On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
>     > Yes,
>     > this is what I have already done: I moved both the
fsaverage and the
>     > subjects into SUBJECTS_DIR and the error I get is ERROR:
source
>     volume
>     > is neither source nor target of the registration.
>     >
>     > On 7 November 2017 at 15:11, Douglas Greve
>     
>
>     > 
>          >
>     >     When you look in SUBJECTS_DIR,  you should see
fsaverage and all
>     >     the subjects being passed to mris_preproc. If not, you
need to
>     >     move them (or sym link them) into that folder.
>     >
>     >
>     >     On 11/7/17 6:07 AM, Elisa Castaldi wrote:
>     >>     Thanks for your answer.
>     >>     If I don't specify the directory I get the following
error
>     >>     ERROR: cannot find fsaverage in SUBJECTS_DIR
>     >>
>     >>     and if I move fsaverage to SUBJECTS_DIR it says that
it cannot
>     >>     find manat_mp1 which is the name of the folder
containing the
>     >>     results of recon all for the subject sub01 (contained
in the
>     >>     SUBJECTS_DIR/surfaces folder). If then I move the
manat_mp1
>     >>     folder into SUBJECTS_DIR it starts running, but then
gives the
>     >>     following error ERROR: source volume is neither
source nor
>     target
>     >>     of the registration.
>     >>     Below the entire list of output printed before the error
>     >>
>     >>     mris_preproc --out lh.con.mgh --target fsaverage
--hemi lh \
>     >>     > --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
>     >>     ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
>     >>     nsubjects = 1
>     >>     tmpdir is ./tmp.mris_preproc.30824
>     >>     SUBJECTS_DIR
>     >>     Log file is lh.con.mris_preproc.log
>     >>
>     >>     setenv SUBJECTS_DIR
>     >>     cd /SUBJECTS_DIR
>     >>     /i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh
>     --target
>     >>     fsaverage --hemi lh --iv
/SUBJECTS_DIR/sub01/stats/con_0001.nii
>     >>     /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
>     >>
>     >>     $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45
zkaufman Exp $
>     >>     freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>     >>     tmpdir is ./tmp.mris_preproc.30824
>     >>     Src lh sphere.reg
>     >>     Trg lh sphere.reg
>     >>
>     >>     ---
>     >>     #@# 1/1 manat_mp1  --
>     >>     ---
>     >>     mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii
>     >>     --srcreg /SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi
lh --out
>     >>     ./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex
--noreshape
>     >>     srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
>     >>     srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> 

Re: [Freesurfer] Creating cached versions of Xhemi registrations

[Douglas Greve]

That looks right, though I'm not sure what is in the design matrix. Is 
it a column of +1 and -1?



On 11/9/17 12:29 PM, Mehta, Chintan wrote:


Dear Doug,

I think that is essentially what I figured. Based on remarks in other 
posts, my steps for evaluating laterality index entail applying:



(1). Apply mri_preproc for each subject $SUB and $meas (area or 
thickness) individually using -xhemi flag but without any paired 
differences via:
> mris_preproc --target fsaverage_sym --hemi lh --xhemi --srcsurfreg 
fsaverage_sym.sphere.reg --meas $meas --out  ${SUB}_out.mgh --s $SUB
Result is a surface file with two volumes (lh and xhemi-lh) called 
${SUB}_out.mgh for each subject.


(2). Smooth the two volumes in ${SUB}_out.mgh at a given $fwhm (5, 10, 
15...):
> mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 
$fwhm  --i ${SUB}_out.mgh --o ${SUB}_out-sm${fwhm}.mgh
to create a surface file with two volumes whose values are smoothed at 
fwhm = $fwhm.


(3). Compute laterality index over the surface for each subject via 
paired-diff-norm:
> mri_concat ${SUB}_out-sm${fwhm}.mgh --paired-diff-norm --o 
${SUB}_latIndex-sm${fwhm}.mgh
where ${SUB}_latIndex-sm${fwhm}.mgh is the surface file with 
laterality index for subject $SUB (after smoothing measures over left 
and right hemispheres).


(4). Stack laterality indices for each subject in sample G  (of n 
subjects) into a single mgh,
> mri_concat --i SUB1_latIndex-sm${fwhm}.mgh --i SUB2_latIndex-sm${fwhm}.mgh ... 
--i SUBn_latIndex-sm${fwhm}.mgh --out --i sampleG_latIndex-sm${fwhm}.mgh.


(5) Run glm with designed matrix sampleG_design.txt containing n rows 
of covariates for SUB1, SUB2, ..., SUBn (in order) via:
> mri_glmfit --y sampleG_latIndex-sm${fwhm}.mgh --X $sampleG_design.txt --no-rescale-x 
--glmdir glm_sampleG --C con1.mat --surf fsaverage_sym lh


The whole purpose of this exercise + question was that I need to 
fit the GLM over subsets of the sample for sensitivity analysis to 
determine whether significance for the contrast in con1.mat (say slope 
of an IV, such as age) depends on patterns of based on demographics 
groups (such as gender). I suppose alternatively, I could just as well 
fit another GLMs with a design matrix modeling interactions between 
age and gender to make my evaluation, over the same set of stacked 
surfaces for the full sample.


Thank you.

Best,
Chintan

1.




___
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


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] dt_recon and Tracula

[Douglas Greve]

Can you send the command line and terminal output?


On 11/10/17 1:34 PM, Mehta, Chintan wrote:


Dear FreeSurfer users,

Sorry for adding the questions, I found most of my answers at

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIDataAnalysisProcessingStream

I used FreeView and found that registrations of the lowb.nii, 
orig.mgz, lh.white, and rh.white aligned very nicely. Alignments 
of lowb.nii with wmparc.mgz and aparc+aseg.mgz are also very nice.


However, I'm finding that resampling wmparc.mgz to diffusion space via 
mri_vol2vol (inverse of dti/register.dat with nearest neighbor 
interpolation) yields poor alignments with the white surfaces 
and lowb.nii. Is this inevitable if there is a difference in 
resolutions between DWI and T1-weighted MRI?


Thank you.

Best,
Chintan




___
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


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] Optseq and de convolution for rapid designs

[Douglas Greve]

It is because the random jitter creates differential amounts of overlap. 
Imagine if you have A=C+D and B=C-D. You know A and B, but you want C 
and D. You have two equations and two unknowns, so you can solve for C 
and D from A and B eventhough C and D "overlap" in A and B and you never 
see C or D by themselves. This is a type of deconvolution



On 11/10/17 11:38 AM, Aser A wrote:

Hi all

I used Optseq  to optimize rapid event designs with multiple 
conditions . I have a theortical question : how it is possible to 
distingwoh the close by trials ? Is it by de convoution ? How is it 
possible to deal with overallped trials ?


Is it because the conditions are random so that when averaging them 
the distingwoh is possible?


Many thanks

Aser



___
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


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] dt_recon and Tracula

[Mehta, Chintan]

Dear FreeSurfer users,

Sorry for adding the questions, I found most of my answers at

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIDataAnalysisProcessingStream

I used FreeView and found that registrations of the lowb.nii, orig.mgz, 
lh.white, and rh.white aligned very nicely. Alignments of lowb.nii with 
wmparc.mgz and aparc+aseg.mgz are also very nice.

However, I'm finding that resampling wmparc.mgz to diffusion space via 
mri_vol2vol (inverse of dti/register.dat with nearest neighbor interpolation) 
yields poor alignments with the white surfaces and lowb.nii. Is this inevitable 
if there is a difference in resolutions between DWI and T1-weighted MRI?

Thank you.

Best,
Chintan


___
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.

Re: [Freesurfer] hemisphere analysis

[Douglas Greve]

Don't use --conjunct, just mri_concat file1 file2 ... file N --o output


On 11/10/17 12:56 PM, lanbo Wang wrote:
I firstly did mris_preproc separately. Secondly used fscalc to reverse 
left symptom subjects. Thirdly used mri_concat --conjunct to combine 
all the subjects together.


The code is:
1.mris_preproc --target fsaverage_sym --hemi lh \
  --xhemi --paired-diff \
  --srcsurfreg fsaverage_sym.sphere.reg \
  --meas thickness \
  --out lh.lh-rh.thickness.sm00.s02.mgh \
  --s subj_02_1
2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o 
lh.lh-rh.thickness.sm00.s09.mgh
3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh 
lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh 
lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh 
lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh 
lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh 
lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh 
lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh 
lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh 
lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh 
lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh 
lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh 
lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh 
lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh 
lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh

4.smooth
5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir 
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh



On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve 
> wrote:


Do you only have one subject in your input file? You need to run
mris_preproc separately for each subject, create a different file
for each, then mri_concat the files together


On 11/9/17 6:20 PM, lanbo Wang wrote:

Dr. Douglas,

I try #3 method, when I run mri_glmfit, get error.
The code I used:
[mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y
lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10
--osgm --surf fsaverage_sym lh
Reading source surface
/HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area 61972.710938
AvgVtxArea   0.378247
AvgVtxDist   0.693419
StdVtxDist   0.190498

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user mtobia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh
logyflag 0
usedti  0
labelmask 
/HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label
maskinv 0
glmdir glm.lh.lh-rh.thickness.sm10
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory glm.lh.lh-rh.thickness.sm10
Loading y from
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh
Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 146902 points in label.
Pruning voxels by thr: 0.00
Found 146902 voxels in mask
Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
Reshaping mriglm->mask...
search space = 79288.081914
DOF = 0
ERROR: DOF = 0

The code I used before this one is
How can I resolve this problem.

Thanks,
Lanbo


On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve
> wrote:

which code. I gave 3 options below, which one did you use?


On 11/07/2017 02:43 PM, lanbo Wang wrote:
> I try to use this code to compare left and right hemisphere
by paired
> t-test  and add age as covariate.
>
> Thanks,
> Lanbo
>
> On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
> 
>> wrote:
>
>     which method are you trying to implement? If #3, then
you need to run
>     mris_preproc separately for each subject, and then run
that fscalc
>     command
>
>
>     On 11/07/2017 11:33 AM, lanbo Wang wrote:
>     > Hi Douglas,
>     >
>     > Thanks for your reply.
>     > I created the fsgd file as you show me, and run code
like this. Am I

Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

I firstly did mris_preproc separately. Secondly used fscalc to reverse left
symptom subjects. Thirdly used mri_concat --conjunct to combine all the
subjects together.

The code is:
1.mris_preproc --target fsaverage_sym --hemi lh \
  --xhemi --paired-diff \
  --srcsurfreg fsaverage_sym.sphere.reg \
  --meas thickness \
  --out lh.lh-rh.thickness.sm00.s02.mgh \
  --s subj_02_1
2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o
lh.lh-rh.thickness.sm00.s09.mgh
3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh
lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh
lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh
lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh
lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh
lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh
lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh
lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh
lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh
lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh
lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh
lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh
lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh
lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh
4.smooth
5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh


On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve 
wrote:

> Do you only have one subject in your input file? You need to run
> mris_preproc separately for each subject, create a different file for each,
> then mri_concat the files together
>
> On 11/9/17 6:20 PM, lanbo Wang wrote:
>
> Dr. Douglas,
>
> I try #3 method, when I run mri_glmfit, get error.
> The code I used:
> [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y
> lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm
> --surf fsaverage_sym lh
> Reading source surface /HD4/subjects_results_symptom/
> /fsaverage_sym/surf/lh.white
> Number of vertices 163842
> Number of faces327680
> Total area 61972.710938
> AvgVtxArea   0.378247
> AvgVtxDist   0.693419
> StdVtxDist   0.190498
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
> cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
> glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
> sysname  Linux
> hostname localhost.localdomain
> machine  x86_64
> user mtobia
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 1
> y/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.
> thickness.sm10.mgh
> logyflag 0
> usedti  0
> labelmask  /HD4/subjects_results_symptom//fsaverage_sym/label/lh.
> cortex.label
> maskinv 0
> glmdir glm.lh.lh-rh.thickness.sm10
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory glm.lh.lh-rh.thickness.sm10
> Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.
> thickness.sm10.mgh
> Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
> Normalized matrix condition is 1
> Matrix condition is 1
> Found 146902 points in label.
> Pruning voxels by thr: 0.00
> Found 146902 voxels in mask
> Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
> Reshaping mriglm->mask...
> search space = 79288.081914
> DOF = 0
> ERROR: DOF = 0
>
> The code I used before this one is
> How can I resolve this problem.
>
> Thanks,
> Lanbo
>
>
> On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve  > wrote:
>
>> which code. I gave 3 options below, which one did you use?
>>
>>
>> On 11/07/2017 02:43 PM, lanbo Wang wrote:
>> > I try to use this code to compare left and right hemisphere by paired
>> > t-test  and add age as covariate.
>> >
>> > Thanks,
>> > Lanbo
>> >
>> > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
>> > > wrote:
>> >
>> > which method are you trying to implement? If #3, then you need to
>> run
>> > mris_preproc separately for each subject, and then run that fscalc
>> > command
>> >
>> >
>> > On 11/07/2017 11:33 AM, lanbo Wang wrote:
>> > > Hi Douglas,
>> > >
>> > > Thanks for your reply.
>> > > I created the fsgd file as you show me, and run code like this.
>> Am I
>> > > right?
>> > > 1.
>> > > mris_preproc --fsgd Subject.xhemi.dat \
>> > >   --target fsaverage_sym --hemi lh \
>> > >   --xhemi --paired-diff \
>> > >   --srcsurfreg fsaverage_sym.sphere.reg \
>> > >   --meas thickness \
>> > >   --out lh.lh-rh.thickness.age.sm00.mgh \
>> > >  --s subj_02_1  --s subj_04_1  --s subj_05_1  --s subj_06_1  --s
>> > > subj_08_1  --s subj_09_1  --s subj_10_1 --s subj_11_1  --s
>> > subj_12_1
>> > > --s subj_13_1  --s subj_14_1  --s subj_15_1  --s subj_16_1 

[Freesurfer] dt_recon and Tracula

[Mehta, Chintan]

Dear FreeSurfer users,

I've been using FreeSurfer and Tracula versions 6.0. I've run Tracula on DWI 
scans, and now I am seeking to run dt_recon on them as well. As a new user, it 
seems both programs follow similar initial pre-processing steps (eddy current & 
motion correction), which the documentation says can take 1-2 hours. I'd 
imagine that these steps not need be repeated for running dt_recon if Tracula 
has already been run.


I have a few questions:

Q1: I ran dt_recon per documentation and the full process finished without 
error within 20 minutes for several initial DWI scans I ran. This is concerning 
since the documentation estimates eddy current & motion correction by itself to 
take 1-2 hours. Is 20 minutes reasonable?

Q2: Is there a way to compare outputs from dt_recon & Tracula to ensure 
consistency in both processes? For example, can I compare stats in the 
fa.nii.gz file? I compared snapshots (attached) of wmparc (from recon-all of 
T1-weighted MRIscan), fa.nii.gz (from dt_recon), and dtifit_FA.nii (from 
Tracula) at the same slice. There are clear differences between dt_recon and 
Tracula that also hold at other slices.

I believe Tracula registers DWI data to subject's anatomical space from 
recon-all of T1-weighted scans. That explains why higher fractional anisotropy 
values (white) in dtifit_FA.nii lined up more nicely with white matter in 
wmparc.nii than that of fa.nii.gz from dt_recon. I want to use mri_segstats on 
the fa.nii from dt_recon (along lines of 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37032.html). 
Does this require first registering fa.nii to subject's native space to create 
a "fa-anat.nii" file? If so, how can I do that? Do I apply an inverse transform 
from the talairach registration of this data (fa-tal.nii.gz) to native space 
via  ${SUB}/mri/transforms/talairach.lta?

Q3: One post on the FreeSurfer Forum suggests that, if dt_recon is run first, 
then Tracula should still be run from the start because trac-all --preproc 
prepares data in an orientation that FSL's bedpostx is expecting.  
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-March/023081.html  
However, does the inverse also hold? If I've run TRACULA (all three steps), is 
there a way to run dt_recon in a way that can allow using the output TRACULA's 
initial steps?

Thank you.

Best,
Chintan
___
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] Optseq and de convolution for rapid designs

[Aser A]

Hi all

I used Optseq  to optimize rapid event designs with multiple conditions . I
have a theortical question : how it is possible to distingwoh the close by
trials ? Is it by de convoution ? How is it possible to deal with
overallped trials ?

Is it because the conditions are random so that when averaging them the
distingwoh is possible?

Many thanks

Aser
___
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.

Re: [Freesurfer] hemisphere analysis

[Douglas Greve]

Do you only have one subject in your input file? You need to run 
mris_preproc separately for each subject, create a different file for 
each, then mri_concat the files together



On 11/9/17 6:20 PM, lanbo Wang wrote:

Dr. Douglas,

I try #3 method, when I run mri_glmfit, get error.
The code I used:
[mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y 
lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 
--osgm --surf fsaverage_sym lh
Reading source surface 
/HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white

Number of vertices 163842
Number of faces    327680
Total area 61972.710938
AvgVtxArea   0.378247
AvgVtxDist   0.693419
StdVtxDist   0.190498

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir 
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh

sysname  Linux
hostname localhost.localdomain
machine  x86_64
user mtobia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y 
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh

logyflag 0
usedti  0
labelmask 
/HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label

maskinv 0
glmdir glm.lh.lh-rh.thickness.sm10
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory glm.lh.lh-rh.thickness.sm10
Loading y from 
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh

Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 146902 points in label.
Pruning voxels by thr: 0.00
Found 146902 voxels in mask
Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
Reshaping mriglm->mask...
search space = 79288.081914
DOF = 0
ERROR: DOF = 0

The code I used before this one is
How can I resolve this problem.

Thanks,
Lanbo


On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve 
> wrote:


which code. I gave 3 options below, which one did you use?


On 11/07/2017 02:43 PM, lanbo Wang wrote:
> I try to use this code to compare left and right hemisphere by
paired
> t-test  and add age as covariate.
>
> Thanks,
> Lanbo
>
> On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
> 
>> wrote:
>
>     which method are you trying to implement? If #3, then you
need to run
>     mris_preproc separately for each subject, and then run that
fscalc
>     command
>
>
>     On 11/07/2017 11:33 AM, lanbo Wang wrote:
>     > Hi Douglas,
>     >
>     > Thanks for your reply.
>     > I created the fsgd file as you show me, and run code like
this. Am I
>     > right?
>     > 1.
>     > mris_preproc --fsgd Subject.xhemi.dat \
>     >   --target fsaverage_sym --hemi lh \
>     >   --xhemi --paired-diff \
>     >   --srcsurfreg fsaverage_sym.sphere.reg \
>     >   --meas thickness \
>     >   --out lh.lh-rh.thickness.age.sm00.mgh \
>     >  --s subj_02_1  --s subj_04_1  --s subj_05_1  --s
subj_06_1  --s
>     > subj_08_1  --s subj_09_1  --s subj_10_1 --s subj_11_1  --s
>     subj_12_1
>     > --s subj_13_1  --s subj_14_1  --s subj_15_1  --s
subj_16_1  --s
>     > subj_17_1 --s subj_18_1  --s subj_20_1 --s subj_21_1  --s
>     subj_22_1
>     > --s subj_24_1  --s subj_25_1  --s subj_26_1 --s subj_27_1  --s
>     > subj_29_1  --s subj_32_1
>     >
>     > 2.
>     > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir
>     > glm.lh.lh-rh.thickness.age.sm10 \
>     > --fsgd Subject.xhemi.dat \
>     > --C Avg-thickness-age-Cor.mtx \
>     > --surf fsaverage_sym lh
>     >
>     > Attachment is fsgd and Avg-thickness-age-cor.mtx.
>     >
>     > All best,
>     > Lanbo Wang
>     >
>     >
>     > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl
>     > 
>
>     
>          >
>     >     Hi Danny
>     >
>     >     you need to give us more information if you want us to
help you.
>     >     Please include the command you ran and the entire
screen output.
>     >
>     >     cheers
>     >     Bruce
>     >
>     >
>     >     On Tue, 7 Nov 2017, Danny Deng wrote:
>     >
>     >         Dear FDs,
>     >         I encountered an odd situation:
>     >
>     >         My free surfer will 

Re: [Freesurfer] comparing sphere and sphere.reg

[Bruce Fischl]

Hi Tony

typically you don't measure distortion by total displacement as if you 
rotate the sphere the displacement would be large but you would not incur 
any distortion.


There are a bunch of measures that try to summarize distortion, but 
basically there is areal and angular distortion that can be combined in 
different summary measures. Areal you can measure by first normalizing the 
two surfaces to have the same total area (not needed in the sphere 
comparison, but if you want to compare to e.g. white you would need to), 
then look at the ratio of the area of each triangle. Angular you can 
compare directly. There are other measures like harmonic energy you can 
also look at.


cheers
Bruce


 On Fri, 10 Nov 2017, tony han wrote:



Hi Bruce,


Thanks for your quick response! So I have several follow-up questions:


1. As I load the two files (.sphere and .sphere.reg), there are two variables 
for each file, i.e.
coordinates and facets. If I want to measure the distortion during 
registration, I will only need to
look at coordinates? If so, the most appropriate way is simply calculating the 
Euclidean distance
for each vertex between the two files (i.e., compute the distance between the 
first row
of coordinates in .sphere file and the first row of coordinates in .sphere.reg, 
and so forth)?


2. What file I can use to get the distortion by the sphere inflation, as you 
mentioned? 


3. The measure of vertex-wise distortion is basically how far each vertex has 
been warped from its
original coordinate (native space) to the new coordinate (fsaverage space)? 
Thanks!


Best,

Tony





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Thursday, November 9, 2017 12:28:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing sphere and sphere.reg  
Hi Tony

you can do that but it won't measure the distortion induced by the sphere
mapping itself.

cheers
Bruce

On Thu, 9 Nov 2017, tony han wrote:

>
> Hi,
>
>
> I'm trying evaluating the distortion for each subject from their native space 
to fsaverage atlas
> space. Is it a appropriate measure to compare ?h.sphere and ?h.sphere.reg? I 
assume that by
> comparison, I may get the how each vertex warped during the registration? 
Thanks!
>
>
> Best,
>
> Tony
>
>
>
>

___
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.

Re: [Freesurfer] comparing sphere and sphere.reg

[tony han]

Hi Bruce,


Thanks for your quick response! So I have several follow-up questions:


1. As I load the two files (.sphere and .sphere.reg), there are two variables 
for each file, i.e. coordinates and facets. If I want to measure the distortion 
during registration, I will only need to look at coordinates? If so, the most 
appropriate way is simply calculating the Euclidean distance for each vertex 
between the two files (i.e., compute the distance between the first row of 
coordinates in .sphere file and the first row of coordinates in .sphere.reg, 
and so forth)?


2. What file I can use to get the distortion by the sphere inflation, as you 
mentioned?


3. The measure of vertex-wise distortion is basically how far each vertex has 
been warped from its original coordinate (native space) to the new coordinate 
(fsaverage space)? Thanks!


Best,

Tony





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Thursday, November 9, 2017 12:28:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing sphere and sphere.reg

Hi Tony

you can do that but it won't measure the distortion induced by the sphere
mapping itself.

cheers
Bruce

On Thu, 9 Nov 2017, tony han wrote:

>
> Hi,
>
>
> I'm trying evaluating the distortion for each subject from their native space 
> to fsaverage atlas
> space. Is it a appropriate measure to compare ?h.sphere and ?h.sphere.reg? I 
> assume that by
> comparison, I may get the how each vertex warped during the registration? 
> Thanks!
>
>
> Best,
>
> Tony
>
>
>
>
___
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.

Re: [Freesurfer] Freeview Crashes!!

[Ruopeng Wang]

What version of freesurfer did you run? It looks like the issue is related to 
incompatible/missing libraries.

Ruopeng

> On Nov 10, 2017, at 7:18 AM, vin rasa  wrote:
> 
> Dear FS Experts,
> 
> While using updated Freeview in ubuntu 16.04, I reproducibly get two 
> following errors:
> 
> 1st Crash (While selecting color for the volume): 
> Volume - Colormap -Lookup Table option: 
> 
> 0�freeview.bin: symbol lookup error: freeview.bin: undefined symbol: 
> _ZN6QMutex12lockInternalEv
> 
> 
> 2nd Error/Crash: 
> Loaded lh.pial and rh.pial surfaces + a volume activated as an isosurface.
> Now while rotating the 3D window Freeview crashes with following error:
> 
> Did not find any volume info
> p9\d�Did not find any volume info
> p9\d�[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 WS52 by wiki Thu Nov  9 
> 16:29:50 2017
> [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
> 
> #
> 
> I don't think RAM/memory is an issue, as the computer has 65GB RAM. Any other 
> options/update I should try? I am planning to load multiple volumes as 
> isosurface in multiple colors, and show them with lh.pial and rh.pial. 
> 
> Thank you very much
> ___
> 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


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] Compare longitudinal evolution of two vertex-wise data

[Diers, Kersten /DZNE]

Hi,

within the LME toolbox it's not possible to directly compare longitudinal 
courses between different regions.

Kersten

Am 07.11.2017 um 21:43 schrieb Matthieu Vanhoutte :

> Dear experts,
> 
> Do you know if there would be a mean to compare longitudinal evolution of two 
> vertex-wise data (i.e. kind of longitudinal correlation) with LME tools or 
> others ?
> 
> Best regards,
> Matthieu
> ___
> 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

[Freesurfer] Freeview Crashes!!

[vin rasa]

Dear FS Experts,

While using updated Freeview in ubuntu 16.04, I reproducibly get two
following errors:

1st Crash (While selecting color for the volume):
Volume - Colormap -Lookup Table option:

0�freeview.bin: symbol lookup error: freeview.bin: undefined symbol:
_ZN6QMutex12lockInternalEv


2nd Error/Crash:
Loaded lh.pial and rh.pial surfaces + a volume activated as an isosurface.
Now while rotating the 3D window Freeview crashes with following error:

Did not find any volume info
p9\d�Did not find any volume info
p9\d�[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/p
etsc-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 WS52 by wiki Thu Nov  9
16:29:50 2017
[0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/L
inux2-2.3-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

#

I don't think RAM/memory is an issue, as the computer has 65GB RAM. Any
other options/update I should try? I am planning to load multiple volumes
as isosurface in multiple colors, and show them with lh.pial and rh.pial.

Thank you very much
___
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.

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[M del Mar Velasco]

Thanks you anyway, Douglas
___
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.

Re: [Freesurfer] Trans. : VBM question

[m . bahri]

Dear Douglas,

Thank you very much for you answer. I checked all the aparc stat files 
(/Freesurfer/subjects/subjectID/stats/lh.aparc.stats; lh.aparc.a2009s.stats 
) and my region of interest "perirhinal" (region extending on BA35 and BA36 
areas) is only present on the lh/rh.BA.stats files 
(/Freesurfer/subjects/subjectID/stats/lh.BA.stats and rh.BA.stats). I use 
Freesurfer version 5.3. When using Qdec tool the only uploadable files are 
.aparc files. Is it possible to upload also the regions of BA.stats files?

Best regards,
Mohamed 

- Mail original -
De: "Douglas N Greve" 
À: "Mohamed Ali Bahri" , freesurfer@nmr.mgh.harvard.edu
Envoyé: Lundi 6 Novembre 2017 23:44:43
Objet: Re: [Freesurfer] Trans. : VBM question

Hi Mohamed, please remember to post to the list. As for your question, 
what aparc files are you looking at? Those measures are in, eg, 
lh.aparc.stats


On 11/06/2017 04:05 AM, Mohamed Ali Bahri wrote:
>
> Dear Douglas,
>
> Many thanks for your answer!
>
> We are interested on one region belonging to the Brodmann areas 
> "Perirhinal". Cortical thickness as well as volume values appear on 
> the BA stat list and not on the aparc or aseg lists. Does the 
> ROI-based analysis could be used for this BA region?
>
> Best regards,
>
> Mohamed
>
>
> On 05/11/2017 18:46, Douglas Greve wrote:
>>
>> Do you just want to do an ROI analysis? Or do you want to do a 
>> voxel-based analysis? If ROI-based, then follow the steps on the ROI 
>> tutorial (ie, aparcstats2table and mri_glmfit with --table input).
>>
>>
>> On 11/3/17 4:08 PM, Bruce Fischl wrote:
>>> Hi Mohamed
>>>
>>> Doug is away this week and can give you a more details answer next 
>>> week. Certainly you could use mris_anatomical_stats -l >> file name> to compute the volume/thickness/area for each subject 
>>> then do whatever GLM analysis you want outside of FS.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>  On Fri, 3 Nov 2017, m.ba...@uliege.be wrote:
>>>
 Dear All,
 Does anyone have an answer to the following VBM question?

 Many thanks in advance,
 Regards

 -Mail original-
 De: "Mohamed Ali Bahri" 
 À: "Freesurfer support list" 
 Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM
 Objet: [Freesurfer] VBM question

 Dear Freesurfer users,

 I would like to study the between groups changes of volume/cortical
 thickness of one region (Perirhinal) belonging to the Brodmann 
 areas. I
 tried to do that with Qdec tool but unfortunately Qdec does not 
 load the
 Brodmann areas stat list. I am wondering if I could use the GLM
 formalism with of course regressing out the ITV. Any suggestion/advice
 will be very welcome.

 Many thanks in advance,

 Best regards,

 Mohamed


>>>
>>>
>>> ___
>>> 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
>>
>>
>> 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.
>
> -- 
> Dr. Mohamed Ali Bahri,
> 1er Logisticien de Recherche,
> Cyclotron Research Centre,
> University of Liège, Belgium
> m.ba...@uliege.be

-- 
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