Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Thank you.I confirm, Annotation works fine. However when trying to load label and select .label file.I get the following message: reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)ERROR: LabelMarkSurface: label point 181451 exceeds nvertices 181405[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 darwin12. named by Fri Apr 8 16:47:36 2016[0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --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 Date: Fri, 8 Apr 2016 11:37:29 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces Hi Pablo if it has the extension .label then it is a label not an annotation, and you should load it as such cheers Bruce On Fri, 8 Apr 2016, pablo najt wrote: > Thank you Bruce for the response.Actually the surface works in freeview just > fine. However my second issue about loading annotation continues. > In freeview I clicked on "Annotations" selected inside "label" folder BA1 > and everything Freezes. > Terminal shows endless column of the text below. > Could there be that anything went wrong with the annotations? Any way to > check for this and ideally correct without running entire recon-all again? > Thanks a lot > Pablo > > MRISreadAnnotationIntoArray: vertex index out of range: 1667852576 > i=6C616265, in_array_size=181405 > > annot file: > /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label > > MRISreadAnnotationIntoArray: vertex index out of range: 1814044716 > i=2066726F, in_array_size=181405 > > annot file: > /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label > > MRISreadAnnotationIntoArray: vertex index out of range: 1830843253 > i=626A6563, in_array_size=181405 > > annot file: /Vo > > > > From: fis...@nmr.mgh.harvard.edu > Date: Fri, 8 Apr 2016 09:56:46 -0400 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces > > Can you check and see if they look ok with freeview? It might just be a > display problem > > On Apr 8, 2016, at 9:26 AM, pablo najt wrote: > > Dear FS expert and users, > We are coming across errors on the WM and Gray inflated surfaces. > When trying to open the surfaces with tksurfer as follows (tksurfer > subid lh inflated -gray) > We get only a small part of the cortex displaying. > > > > > Also when we try file-label-import annotation the following error > occurs: > colortable with 13 entries read (originally > /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt) > Found
Re: [Freesurfer] errors on the WM and Gray inflated surfaces
Thank you Bruce for the response.Actually the surface works in freeview just fine. However my second issue about loading annotation continues.In freeview I clicked on "Annotations" selected inside "label" folder BA1 and everything Freezes.Terminal shows endless column of the text below. Could there be that anything went wrong with the annotations? Any way to check for this and ideally correct without running entire recon-all again?Thanks a lotPablo MRISreadAnnotationIntoArray: vertex index out of range: 1667852576 i=6C616265, in_array_size=181405 annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label MRISreadAnnotationIntoArray: vertex index out of range: 1814044716 i=2066726F, in_array_size=181405 annot file: /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label MRISreadAnnotationIntoArray: vertex index out of range: 1830843253 i=626A6563, in_array_size=181405 annot file: /Vo From: fis...@nmr.mgh.harvard.edu Date: Fri, 8 Apr 2016 09:56:46 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces Can you check and see if they look ok with freeview? It might just be a display problem On Apr 8, 2016, at 9:26 AM, pablo najt wrote: Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. Also when we try file-label-import annotation the following error occurs:colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found embedded color table in annotation. There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate.Now we are trying to figure what is that could have caused this for all subjects.We have an old instructions for freesurfer saying to to run recon-all as follows.run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo ___ 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.___ 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] errors on the WM and Gray inflated surfaces
Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. Also when we try file-label-import annotation the following error occurs:colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found embedded color table in annotation. There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate.Now we are trying to figure what is that could have caused this for all subjects.We have an old instructions for freesurfer saying to to run recon-all as follows.run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo ___ 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] Difficulty correcting Pial surfaces
Dear experts and FS users,I came across the following problem it would be useful help if anyone is able to advice.ThanksPablo I am having issues when trying to remove non cortical tissue (mostly skull). I load my images as follow: freeview -v mri/T1.mgz mri/brainmask.mgz -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=r "invalid drawable" error is displayed. Then I have tried to follow the guide in the tutorial 'Correcting Pial Surfaces'Selected Recon edit free hand option, selected brain mask.mgz hold down the Shift key and left click. This does not change the surface.I am wondering if there is a different key shortcut with O SX. Or if there is anything else I could try. I also tried older instructions with tkmedik and I have the same problem.Any advice will be greatly appreciated.Thanks, Pablo ___ 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 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] Difficulty correcting Pial surfaces
Dear FS experts.I am having issues when trying to remove non cortical tissue (mostly skull). I load my images as follow: freeview -v mri/T1.mgz mri/brainmask.mgz -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=r Then I have tried to follow the guide in the tutorial 'Correcting Pial Surfaces'Selected Recon edit free hand option, selected brain mask.mgz hold down the Shift key and left click. This does not change the surface.I am wondering if there is a different key shortcut with O SX. Or if there is anything else I could try. I also tried older instructions with tkmedik and I have the same problem.Any advice will be greatly appreciated.Thanks, Pablo ___ 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] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}
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
Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
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%
Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
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?ThanksPablo
[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 "age"
columns".
4-Perform vertex-wise inference eg.:
CM.C = [your contrast matrix];
F_lhstats = lme_mass_F(lhstats, CM);
5-Save results eg.:
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');
Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A mixed effect model approach in within subject
dataset
Hi Pablo
I think you can use
LME to analyze your data by ordering the rows of your design matrix
appropriately. You can consider all subjects belonging to the same
family as if they were a single subject in a longitudinal analysis.
You can put in your design matrix all subjects belonging to family1
first, then all subjects belonging to family 2 and so on. Then the
'ni' required by lme_mass_fit_vw is a vector with the number of
subjects in each family as its entries (ordered according to your
design matrix). So the length of the 'ni' vector is equal to the
number of different families in your data.
Now you can go
further and additionally order the rows of your design matrix within
each family by age.
[Freesurfer] Display pctdiff only cluster surviving multiple comparisons
Thank you, Doug.I have computed the percent difference between a 2-group comparison. However when I open the results the percent difference is showing all over the cortex. Instead I would like to only display the percent difference in the area that survived multiple comparisons. Is there a way I can use that cluster for displaying the pctdiff.mgh? I am using tksurfer for this.Thanks!Pablo ___ 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] Contrast for a group diff correlation with age
Hello FS experts,I have a question about setting the following contrast in mri_glmfitMy contrast of interest:Does area.pial --age correlation, accounting for gender, differ between PT and HC? Class Female_PTClass Female_HCClass Male_PTClass Male_HCIf I set my classes are as above, should my contrast be the following: fem_PT, fem_HC, male_PT, male_HC, age1 -1 1 -1 0 ThanksPablo ___ 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] Volumes differ in acquisition paramaters
Dear Martin and FS experts.I am having difficulty in loading my qdec.table.dat
to Matlab.When I use the [command: Qdec = fReadQdec('qdec.table.dat'); ] Matlab
only recognises a matrix of 140x1 cell, whereas instead it should recognise a
140x4.I tried to import the table as 'table' from the gui interface but then I
am getting error on the command: M = Qdec2num(Qdec,1) Any tips on how to load
my table would be fabulous help.Thank youPabloTo: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Mon, 19 Oct 2015 09:04:41 -0400
Subject: Re: [Freesurfer] Volumes differ in acquisition paramaters
Hi Kasper,
if you use the same file formats and conversion tools across both
time points, the images should be identical. Even after conversion
to nii. Not sure why they are not.
Yes, both warnings are related to the acquisition parameters. The
second should better say that header information is different or
something like that. I see if I can improve that error message to be
more specific in a future release.
Best, Martin
On 10/17/2015 08:59 AM, Kasper Jessen
wrote:
Hi Bruce,
Thank you for your reply.
Initially
a PAR/REC file was used to obtain an anat.nii file. This is
used to create the
[CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) was used
to create the [BASE].
Is it because there is too many file formats, and if so,
how should this be managed? Is it possible to run
freesurfer directly from the PAR/REC file?
Is the
“Image geometries differ across time” related to the
difference in acquisition parameters mentioned
in the warning?
Best regards
Kasper Jessen
2015-10-10 16:12 GMT+02:00 Bruce Fischl
:
Hi Kasper
what was your input volume? The .02sec change in TR won't
mean anything,
although it is a bit surprising to see, as is the fact that
the other
parameters (flip angle, TE, etc...) don't seem to be
preserved. We usually
read those right out of the dicom files if that is what you
used as input.
Not sure why we would preserve the TR but not the other
parameters.
cheers
Bruce
On Sat, 10 Oct 2015, Kasper Jessen wrote:
>
> Dear Freesurfer group,
>
> When looking through the log after running
recon-all, i have noticed two
> different errors in the logs. The one being about
'volumes differ in
> acquisition parameters' and the other 'Image
geometries differ across time,
> maybe due to aquisition changes?'.
>
> Volumes differ in acquisition parameters
> v1acq fa=0.00 tr=10.032000 te=0.00
ti=0.00
> v2acq fa=0.00 tr=10.012000 te=0.00
ti=0.00
> WARNING: Image geometries differ across time, maybe
due to aquisition
> changes?
> This can potentially bias a longitudinal study!
Will continue in 10s.
>
> What do the above errors mean and is it something
we should be worried
> about?
>
> Best regards,
> Kasper Jessen
> MD, PhD Student
>
>
>
___
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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
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Compliance HelpLine at
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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Hi Jorge and FS experts,I have run again the analysis and still get the
convergence problem.I am assuming the issue has to do with the preprocessing
steps, as I had doubts on how to follow from the instructions if I am not using
qdec and have a cross sectional design.
Instructions on lme in the wiki for preprocessing specify the following:
mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas
thickness --out lh.thickness.mghmri_surf2surf --hemi lh --s study_average
--sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex
--noreshapeMy data -as I explained below- is cross section but I want to treat
it as longitudinal as I want to analyse subjects belonging to the same family.
Here is my 2 main questions: 1) for preprocessing should I follow instructions
as it would be longitudinal data?2) Although my design does not allow using
qdec (3 groups) do I still create a qdec table and follow literally the two
instructions above ?Thank youPablo
Date: Fri, 16 Oct 2015 16:24:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablon...@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject
dataset {Disarmed}
Hi Pablo
Yes, too many locations at which the estimation algorithm didn't converge is
problematic. That might mean that having two random effects is not appropriate
for your data. You should try to run the command with just a single random
effect for the intercept term:
lhstats = lme_mass_fit_vw(X, [1], lhY, ni, lhcortex, [], 4);
If the result still have too many non-convergence locations then something
might be wrong with the ordering of the design matrix and its correspondence
with the ordering of the ni vector or the ordering of the image data etc... You
will need to check it thoroughly.
Cheers-Jorge
De: pablo najt
Para: "freesurfer@nmr.mgh.harvard.edu"
Enviado: Viernes 16 de octubre de 2015 1:43
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject
dataset {Disarmed}
Thanks you for the replies.Jorge and FS experts,I have run the analysis and
first double checked that the sum of vectors of (ni) is equal to the number of
rows in (X). Both are 140 which is the number of my subjects.The analysis gave
the following 'error'(?) below:I looked up a previous thread coming across
this. At that case you recommendedWould you recommend this afain>Aproximate
percentage of fitted locations: 100%Warning: matlabpool will be removed in a
future release.To query the size of an already started parallel pool, query the
'NumWorkers'property of the pool.To check if a pool is already started use
'isempty(gcp('nocreate'))'. Warning: matlabpool will be removed in a future
release.To shutdown a parallel pool use 'delete(gcp('nocreate'))' instead.
Parallel pool using the 'local' profile is shutting down. Summary:Algorithm
did not converge at 90.0637 percent of the total number of locations.Total
elapsed time is 550.1023 minutes.Also almost all the time the screen showed the
following message:144114: Algorithm did not converge. Initial and final
likelihoods: -38.3408-1.5708i, -241.4153-1.570796i.Location 144113: Algorithm
did not converge. Initial and final likelihoods: -5.5424-1.5708i,
-133.8004-1.570796i.Location 144112: Algorithm did not converge. Initial and
final likelihoods: -7.7571-1.5708i, -319.1378-1.570796i.Location 144111:
Algorithm did not converge. Initial and final likelihoods: -16.8597-1.5708i,
0.74448.Aproximate percentage of fitted locations: 100%So my two questions
are:1. Is this problematic?2. Are there any fixes to this issue?Thank
you,PabloDate: Thu, 15 Oct 2015 13:38:22 +From: jbernal0...@yahoo.esto:
freesur...@nmr.mgh.harvard.eduCC: pablonajt@hotmail.comSubject: Re:
[Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Hi PabloThe error you are getting is because in your Matlab setup you can only
request a maximum of 4 matlab parallel workers and by default lme requests 8.
So you just need to modify your command like this: lhstats = lme_mass_fit_vw(X,
[1 2], lhY, ni, lhcortex, [], 4);Please make sure that sum(ni) and length(X)
give the same value before running the above command.Cheers-Jorge De:
pablo najt Para: Freesurfer support list
Enviado: Jueves 15 de octubre de 2015 7:18
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject
dataset {Disarmed} Thank you Martin.I am trying to run the following command
line and get the error below. Would you have a suggestion to overcome this
issue?Just in case I am also including a snapshot of my loaded variables at the
bottom.Many thanks,Pablo>> lhstats = lme_mass_fit_vw(X, [1 2], lhY, n
Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Thanks you for the replies.Jorge and FS experts,I have run the analysis and
first double checked that the sum of vectors of (ni) is equal to the number of
rows in (X). Both are 140 which is the number of my subjects.The analysis gave
the following 'error'(?) below:I looked up a previous thread coming across
this. At that case you recommendedWould you recommend this afain>
Aproximate percentage of fitted locations: 100%Warning: matlabpool will be
removed in a future release.To query the size of an already started parallel
pool, query the 'NumWorkers'property of the pool.To check if a pool is already
started use 'isempty(gcp('nocreate'))'. Warning: matlabpool will be removed in
a future release.To shutdown a parallel pool use 'delete(gcp('nocreate'))'
instead. Parallel pool using the 'local' profile is shutting down.
Summary:Algorithm did not converge at 90.0637 percent of the total number of
locations.Total elapsed time is 550.1023 minutes.
Also almost all the time the screen showed the following message:144114:
Algorithm did not converge. Initial and final likelihoods: -38.3408-1.5708i,
-241.4153-1.570796i.Location 144113: Algorithm did not converge. Initial and
final likelihoods: -5.5424-1.5708i, -133.8004-1.570796i.Location 144112:
Algorithm did not converge. Initial and final likelihoods: -7.7571-1.5708i,
-319.1378-1.570796i.Location 144111: Algorithm did not converge. Initial and
final likelihoods: -16.8597-1.5708i, 0.74448.Aproximate percentage of fitted
locations: 100%
So my two questions are:1. Is this problematic?2. Are there any fixes to this
issue?Thank you,Pablo
Date: Thu, 15 Oct 2015 13:38:22 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablon...@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject
dataset {Disarmed}
Hi Pablo
The error you are getting is because in your Matlab setup you can only request
a maximum of 4 matlab parallel workers and by default lme requests 8. So you
just need to modify your command like this:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex, [], 4);
Please make sure that sum(ni) and length(X) give the same value before running
the above command.
Cheers-Jorge
De: pablo najt
Para: Freesurfer support list
Enviado: Jueves 15 de octubre de 2015 7:18
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject
dataset {Disarmed}
Thank you Martin.I am trying to run the following command line and get the
error below. Would you have a suggestion to overcome this issue?Just in case I
am also including a snapshot of my loaded variables at the bottom.Many
thanks,Pablo>> lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);Warning:
matlabpool will be removed in a future release.To query the size of an already
started parallel pool, query the 'NumWorkers'property of the pool.To check if a
pool is already started use 'isempty(gcp('nocreate'))'. Warning: matlabpool
will be removed in a future release.To query the size of an already started
parallel pool, query the 'NumWorkers'property of the pool.To check if a pool is
already started use 'isempty(gcp('nocreate'))'. Warning: matlabpool will be
removed in a future release.Use parpool instead. Starting matlabpool using the
'local' profile ... Error using matlabpool (line 148)Failed to start a parallel
pool. (For information in addition to the causing error,validate the profile
'local' in the Cluster Profile Manager.)Error in lme_mass_fit (line 128)
matlabpool(prs);Error in lme_mass_fit_vw (line 73)[stats1,st1] =
lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);Caused by:Error using
parallel.internal.pool.InteractiveClient/start (line 330)Failed to start
pool.Error using parallel.Job/submit (line 304)You requested a
minimum of 8 workers, but the cluster "local" has theNumWorkers
property set to allow a maximum of 4 workers. To run acommunicating job
on more workers than this (up to a maximum of 512 for theLocal
cluster), increase the value of the NumWorkers property for thecluster.
The default value of NumWorkers for a Local cluster is the number of
cores on the local machine.
To: freesur...@nmr.mgh.harvard.eduFrom: mreu...@nmr.mgh.harvard.eduDate: Wed,
14 Oct 2015 10:54:41 -0400Subject: 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
Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
Thank you Martin.I am trying to run the following command line and get the
error below. Would you have a suggestion to overcome this issue?Just in case I
am also including a snapshot of my loaded variables at the bottom.Many
thanks,Pablo>> lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
Warning: matlabpool will be removed in a future release.To query the size of an
already started parallel pool, query the 'NumWorkers'property of the pool.To
check if a pool is already started use 'isempty(gcp('nocreate'))'. Warning:
matlabpool will be removed in a future release.To query the size of an already
started parallel pool, query the 'NumWorkers'property of the pool.To check if a
pool is already started use 'isempty(gcp('nocreate'))'. Warning: matlabpool
will be removed in a future release.Use parpool instead. Starting matlabpool
using the 'local' profile ... Error using matlabpool (line 148)Failed to start
a parallel pool. (For information in addition to the causing error,validate the
profile 'local' in the Cluster Profile Manager.)
Error in lme_mass_fit (line 128)matlabpool(prs);
Error in lme_mass_fit_vw (line 73)[stats1,st1] =
lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
Caused by:Error using parallel.internal.pool.InteractiveClient/start (line
330)Failed to start pool.Error using parallel.Job/submit (line 304)
You requested a minimum of 8 workers, but the cluster "local" has the
NumWorkers property set to allow a maximum of 4 workers. To run a
communicating job on more workers than this (up to a maximum of 512 for the
Local cluster), increase the value of the NumWorkers property for the
cluster. The default value of NumWorkers for a Local cluster is the number of
cores on the local machine.
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);
Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}
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.ThanksPablo
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 designmatrix 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 "age" columns".
4-Perform vertex-wise inference eg.:
CM.C = [your contrast matrix];
F_lhstats = lme_mass_F(lhstats, CM);
5-Save results eg.:
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');
Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A mixed effect model approach in within subject
dataset
Hi Pablo
I think you can use
LME to analyze your data by ordering the rows of your design matrix
appropriately. You can consider all subjects belonging to the same
family as if they were a single subject in a longitudinal analysis.
You can put in your design matrix all subjects belonging to family1
first, then all subjects belonging to family 2 and so on. Then the
'ni' required by lme_mass_fit_vw is a vector with the number of
subjects in each family as its entries (ordered according to your
design matrix). So the length of the 'ni' vector is equal to the
number of different families in your data.
Now you can go
further and additionally order the rows of your design matrix within
each family by age. This will allow you to test the effect of age
within family.
When choosing the
random effects for your statistical model remember that a random
effect can only be the intercept term or any covariate that varies
within family. For example you can compare a model with a single
random effect for the intercept term against the same model but
considering both the intercept term and age as random effects.
Hope that helps
Cheers
-Jorge
De: pablo najt
Para: "freesurfer@nmr.mgh.harvard.edu"
Enviado: Jueves 10 de septiembre de 2015 8:07
Asunto: [Freesurfer] A mixed effect model approach in within subject dataset
Dear Freesurfer users,I wanted to enquire if anyone had successfully been able
to implement Bernal's Linear Mixed Effects (LME) Models in cross-section
dataset *not longitudinal* (please see previous thread below). I am willing to
perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates
(sex, age, and family) with "family" variable been a within-subject factor. LME
will allow to control for the non-independence of data contributed by patients
and relatives from the same families.Thanks in advance!Pablo
From: michaelnot...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 19 Feb 2014 13:10:09 +0100
Subject: [Freesurfer] Analysis of structural data acquired from multiple sites
by using a mixed effect model approach
Hi everybody,
I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls)
but have the problem that they were acquired from 4 different scanner sites. As
I can see it, there are three ways how I could tackle this problem:
1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes:
Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25
0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the
Controlls. My Problem with this approach is, that the sites don't contribute
the same amount of subjects to the analysis. I'm not sure if this could be
handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had
twice as many subjects than Site3 and Site4, I could modify the contrast to
[0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17].
2.
Re: [Freesurfer] repeated measures ANOVA using the FSGD file
Hello FS experts,I am reposting as a good few emails went by after me posting. My question is below.Thank you for your help.Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 6 Oct 2015 13:53:21 + Subject: [Freesurfer] repeated measures ANOVA using the FSGD file Dear FS expertsTrying to set up a Linear Mixed Effects, which I understand would basically be a repeated measures design. My design has 3 groups (HC, PT relatives and PT).Instead of time points of the same subject my design matrix uses each family member within a family. So I will have many subjects within family_1, same for family_2 and so on...I also want to include gender as a covariate. In short my question is:For my design in repeated measures do I need to define all my groups for each discrete variable as how we do it for glm?For example if I want to have variables GROUP + GENDER + FAMILY.Should i do it as follows?class HC_Female_Family1class PT_Female_Family1class HC_Male_Family2class HC_Female_Family2.. Many thanks,Pablo ___ 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 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] repeated measures ANOVA using the FSGD file
Dear FS expertsTrying to set up a Linear Mixed Effects, which I understand would basically be a repeated measures design. My design has 3 groups (HC, PT relatives and PT).Instead of time points of the same subject my design matrix uses each family member within a family. So I will have many subjects within family_1, same for family_2 and so on...I also want to include gender as a covariate. In short my question is:For my design in repeated measures do I need to define all my groups for each discrete variable as how we do it for glm?For example if I want to have variables GROUP + GENDER + FAMILY.Should i do it as follows?class HC_Female_Family1class PT_Female_Family1class HC_Male_Family2class HC_Female_Family2.. Many thanks,Pablo ___ 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] FSGD for A mixed effect model approach in within subject dataset
Hello JorgeTrying to set up for running Linear Mixed Effects. My design has 3
groups (HC, PT relatives and PT) and therefore I am not using QDEC as suggested
in the tutorial. My first question: Are there any changes from the matlab
commands you suggest in the tutorial if using fsgd rather than Qdec?About my
design matrix you suggested below to use each family as the same subject. So I
will have family_1 as subject_1, family_2 as subject_2... In my fsgd I need to
define at the top the classes and in my matrix these will be the families
(family_1, ...). However I also have a number of discrete variables which I
define within the classes when running my glm, so I am wondering does this mean
that I will be defining my classes as follow?class HC_Female_Family1class
PT_Female_Family1class HC_Male_Family2etc
Many thanks,Pablo
Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A mixed effect model approach in within subject
dataset
Hi Pablo
I think you can use
LME to analyze your data by ordering the rows of your design matrix
appropriately. You can consider all subjects belonging to the same
family as if they were a single subject in a longitudinal analysis.
You can put in your design matrix all subjects belonging to family1
first, then all subjects belonging to family 2 and so on. Then the
'ni' required by lme_mass_fit_vw is a vector with the number of
subjects in each family as its entries (ordered according to your
design matrix). So the length of the 'ni' vector is equal to the
number of different families in your data.
Now you can go
further and additionally order the rows of your design matrix within
each family by age. This will allow you to test the effect of age
within family.
When choosing the
random effects for your statistical model remember that a random
effect can only be the intercept term or any covariate that varies
within family. For example you can compare a model with a single
random effect for the intercept term against the same model but
considering both the intercept term and age as random effects.
Hope that helps
Cheers
-Jorge
De: pablo najt
Para: "freesurfer@nmr.mgh.harvard.edu"
Enviado: Jueves 10 de septiembre de 2015 8:07
Asunto: [Freesurfer] A mixed effect model approach in within subject dataset
Dear Freesurfer users,I wanted to enquire if anyone had successfully been able
to implement Bernal's Linear Mixed Effects (LME) Models in cross-section
dataset *not longitudinal* (please see previous thread below). I am willing to
perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates
(sex, age, and family) with "family" variable been a within-subject factor. LME
will allow to control for the non-independence of data contributed by patients
and relatives from the same families.Thanks in advance!Pablo
From: michaelnot...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 19 Feb 2014 13:10:09 +0100
Subject: [Freesurfer] Analysis of structural data acquired from multiple sites
by using a mixed effect model approach
Hi everybody,
I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls)
but have the problem that they were acquired from 4 different scanner sites. As
I can see it, there are three ways how I could tackle this problem:
1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes:
Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25
0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the
Controlls. My Problem with this approach is, that the sites don't contribute
the same amount of subjects to the analysis. I'm not sure if this could be
handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had
twice as many subjects than Site3 and Site4, I could modify the contrast to
[0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17].
2. I could create dummy variables to account for the variability between sites.
In this case, I only need to specify 3 classes (Class GroupA; Class GroupB;
Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy
variables at the end, which specify to which site a subject belongs. This
approach might work, but I'm not confident that it is the right one.
3. I could use a mixed effect model approach and specify site as a random
effect.
If I understand it correctly, the mixed effect model approach would be the best
one, as it accounts for the variability within sites. Is that correct or are
there other issues/better approaches?
I tried to implement a mixed effect model by using Bernal's Linear Mixed
Effects (LME) Models
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run
into some problems. I'm not sure if LME can only be applied on longitudinal
data or
[Freesurfer] Test incoming emails -
I am sending this message as a test since my income emails from FS stopped working on the 29 of September.Regards ___ 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: group differences covaring for age and sex {Disarmed}
Hello Douglas, If I understand your comment about defining all discrete variables as classes (e.g. PT_F, PT_M, HC_F, HC_M) *only applies* to glm command line stream not qdec. If I am using qdec I can have discrete variables defined separately (e.g. Sex, Diagnosis) specified in the qdec.table text file as I am not required to specify classes as in the FS descriptor file. I am following here the instructions as shown below. Do I understand correct? Thanks, Pablo qdec.table example from FSpage > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Mon, 21 Sep 2015 17:39:14 -0400 > Subject: Re: [Freesurfer] Qdec: group differences covaring for age and sex > > Yes, it is addressing that question. The contrast should be the same as > your Group Diff below. Although I'm not sure you're using the proper > design. It looks like you are using Sex as a continuous covariate? That > is not correct. It should be discrete. So you should have 4 classes > (HC-M, HC-F, PT-M, PT-F) > > On 09/21/2015 09:31 AM, pablo najt wrote: > > Hello FS experts, > > I would like to understand the results from qdec in a GLM model with > > Group (PT/HC), and two covariates (Age, gender). > > I set up my contrast as follow: > > > > Group Diff > > HC PT AgeHC AgePT SexHC SexPT > > 1 -10 0 0 0 > > > > Group x Age effect > > HC PT AgeHC AgePT SexHC SexPT > > 0 0 1 -1 00 > > > > Group X Sex effect > > HC PT AgeHC AgePT SexHC SexPT > > 0 0 0 0 1 -1 > > Continues just as indicated in the "2 Groups 2 Covariates example" > > > > What I would like to find out: /If there are group differences while > > controlling for age and sex/. > > > > In Qdec I selected Group, Gender, and Age. (Age as normal variable, > > not as nuisance) > > However, when I open my results with Qdec I am not quite sure it is > > answering my question. > > > > From all the questions listed I thought that the following was > > addressing what I need, but would like to clarify. > > "/Does the thickness, --Age correlation, accounting for Gender, differ > > between HC and PT?"/ > > Would you mind confirming this for me? > > Thanks!! > > Pablo > > > > > > ___ > > 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 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] Question about the multiple comparison correction in FreeSurfer {Disarmed}
Thank you!
Date: Mon, 21 Sep 2015 23:43:39 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Question about the multiple comparison correction in
FreeSurfer
On 9/21/15 9:15 PM, chenhf_uestc wrote:
Hi, Douglas
Thanks for your reply. I have two further questions here.
First, I know that
--grf is gaussian random fields for the volume (not surface). Could
the Monte Carlo simulation such as "--cache 4 neg" be used for
correction on volume? Because the manual introduces this method
for the correction on surface, and thus I do not whether this
method could be used on volume.
Yes, I think that should work. If you are going to run simulations
on the surface, see
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
Second, in the Monte Carlo simulation on surface
"--cache 4 neg", I can specify the sign (neg for negative, pos,
or abs). However, in the grf correction, there are "--grf 3 pos or neg
". Could I
specify the sign "abs" such as "--grf
3 abs".
No, sorry
Best,
Feng
发件人：Douglas N Greve
发送时间：2015-09-22 05:35
主题：Re: [Freesurfer] Question about the
multiple comparison correction in FreeSurfer
收件人："freesurfer"
抄送：
--grf is gaussian random fields for the volume (not surface).
Re: --2spaces, your understanding is correct.
FDR: you can do it in matlab, something like
sig = MRIread('sig.mgh');
p = 10.^-abs(sig.vol)
pthresh = fast_fdrthresh(p,fdr);
ind = find(p < pthresh);
sig.vol(ind) = 0;
MRIwrite(sig,'sig.fdr.mgh')
It is also possible with mri_surfcluster
On 09/20/2015 12:47 PM, chenhf_uestc wrote:
> Dear Freesurfer experts,
> I have some questions about the multiple comparison correction
method
> for group analysis in Freesurfer. The manual stated that we could
use
> the commands as follows:
> mri_glmfit-sim \
>--glmdir lh.gender_age.glmdir \
>--cache 4 neg \
>--cwp 0.05\
>--2spaces
> This is the alphasim correction, right? When I write this command
in
> terminal, there are detailed explanations about this command. In
the
> above-mentioned command, I used parameter "--cache threshold sign".
In
> this way, a precomputed Z Monte Carlo simulation (--cache) was
used.
> Also, I can run my own simulation by using "--sim mc-z
> iterations threshold".
> However, I find an interesting parameter "--grf threshold sign". I
> would like to know whether this parameter could give me another
> correction method rather than alphasim, i.e. the gaussian random
field
> correction method? In other words, if I add the parameter "grf",
then
> the mri_glmfit-sim performs the GRF correction; if I do not add
this
> parameter, then mri_glmfit-sim performs alphasim correction, right?
> Another question is about the parameter "--2spaces: adjust p-values
> for two hemispheres", I give an example here. I want to perform
> cluster-level correction of *p<0.05* based on vertex-wise thershold
of
> 4 (p < .0001) for the left hemisphere; and perform the same
correction
> for the right hemisphere. So, I should add the parameter
"--2spaces".
> Is this equal to perform cluster-level correction of *p<0.025
(0.05/2,
> if I also want to examine the subcortical diferences, then the
cluster
> p value should be 0.05/3)* based on vertex-wise thershold of 4 (p <
> .0001). Have I understood correctly?
> The third question is that could I perform False discovery rate
(FDR)
> using commands rather than GUI? If not, could I load the sig.mgh
file
> into MatLab and then perform FDR correction manually?
> In addition to the aforementioned multiple comparison correction
> method, is there other correction method in Freesurfer?
> Best,
> Feng
>
>
> ___
> 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.harva
[Freesurfer] Qdec: group differences covaring for age and sex
Hello FS experts,I would like to understand the results from qdec in a GLM model with Group (PT/HC), and two covariates (Age, gender).I set up my contrast as follow: Group DiffHC PT AgeHC AgePT SexHC SexPT 1 -10 0 0 0 Group x Age effectHC PT AgeHC AgePT SexHC SexPT 0 0 1 -1 00 Group X Sex effectHC PT AgeHC AgePT SexHC SexPT 0 0 0 0 1 -1Continues just as indicated in the "2 Groups 2 Covariates example" What I would like to find out: If there are group differences while controlling for age and sex. In Qdec I selected Group, Gender, and Age. (Age as normal variable, not as nuisance)However, when I open my results with Qdec I am not quite sure it is answering my question. >From all the questions listed I thought that the following was addressing what >I need, but would like to clarify."Does the thickness, --Age correlation, >accounting for Gender, differ between HC and PT?"Would you mind confirming >this for me?Thanks!!Pablo___ 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] Magnitude of group difference
Hello Doug,Thanks for the answer, my intention is to compute percent difference between groups in area (and separately for area.pial). About the contrast, you said that in order to compute the percent difference between groups I need to specify a contrast for each group separately (think would be one contrast with group1 as "1" versus "0") and same for group2.As my glm original contrasts have four regressors: (group1, group2, age, sex) I am in doubt if for these two new contrasts for percent difference I still keep my covariates or should get rid of?Thanks! > To: freesurfer@nmr.mgh.harvard.edu > From: gr...@nmr.mgh.harvard.edu > Date: Fri, 18 Sep 2015 15:00:40 -0400 > Subject: Re: [Freesurfer] Magnitude of group difference > > > > On 09/18/2015 02:37 PM, pablo najt wrote: > > Hello Doug, > > Below you suggested that I can calculate percent difference if I > > create a contrast of group1 vs 0 and same group2, for cortical > > thickness. Does this applies to Area and Area.Pial as well? > You mean to compute the percent diff between the white and pial surface > area? yes, that will work. or to look at percent diff between group1 and > group2 for white surface and then for pial surface as well? that will > work too. > > About my contrasts for my qdec analysis I have two levels two covariates > > So my contrasts look: 1 -1 0 0, etc. > > So should I keep the two regressors corresponding to the two variables > > (1 0 0 0)? > > Or it should it be like this:(1 0)? > what is this in reference to? > > Thanks, > > Pablo > > > > > > Date: Fri, 28 Aug 2015 10:41:30 -0400 > > From: gr...@nmr.mgh.harvard.edu > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Magnitude of group difference > > > > There are a couple of things you can do. > > > > You can create a contrast for each group separately, then compute the > > voxel-wise percent difference between the maps, eg, > > fscalc group1/gamma.mgh pctdiff group2/gamma.mgh -o pctdiff.mgh > > > > You can compute the percent differences from the average in the > > cluster. For this you'll need to load the y file for the clusters and > > sort the subjects (rows) into groups and compute the precentage > > difference. > > > > > > > > On 8/28/15 4:54 AM, pablo najt wrote: > > > > Hello FS experts and all, > > I would like to find out the magnitude of the group difference > > between a two-group comparison (e.g. percent difference on > > cortical thickness indicating how much one group differs from the > > other.) I have run analysis using both mri_glmfit and qdec, I also > > run cluster wise correction for multiple comparisons but in my > > summary tables I am not finding this information. Do I need to run > > any additional command to find out about this? > > Thank you > > Pablo > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > > ___ > > 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
Re: [Freesurfer] Magnitude of group difference
Hello Doug, Below you suggested that I can calculate percent difference if I create a contrast of group1 vs 0 and same group2, for cortical thickness. Does this applies to Area and Area.Pial as well? About my contrasts for my qdec analysis I have two levels two covariates So my contrasts look: 1 -1 0 0, etc. So should I keep the two regressors corresponding to the two variables (1 0 0 0)? Or it should it be like this:(1 0)? Thanks, Pablo Date: Fri, 28 Aug 2015 10:41:30 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Magnitude of group difference There are a couple of things you can do. You can create a contrast for each group separately, then compute the voxel-wise percent difference between the maps, eg, fscalc group1/gamma.mgh pctdiff group2/gamma.mgh -o pctdiff.mgh You can compute the percent differences from the average in the cluster. For this you'll need to load the y file for the clusters and sort the subjects (rows) into groups and compute the precentage difference. On 8/28/15 4:54 AM, pablo najt wrote: Hello FS experts and all, I would like to find out the magnitude of the group difference between a two-group comparison (e.g. percent difference on cortical thickness indicating how much one group differs from the other.) I have run analysis using both mri_glmfit and qdec, I also run cluster wise correction for multiple comparisons but in my summary tables I am not finding this information. Do I need to run any additional command to find out about this? Thank you Pablo ___ 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. ___ 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] Resolved - RE: Error downloading fs dataset
Thanks, Realized that using FAT32 there is a file size for individual file of 4GB. So downloading to my tower and will move after unzipping. Thanks P From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 18 Sep 2015 16:18:52 + Subject: Re: [Freesurfer] Error downloading fs dataset Thanks Lee, I thought about this but this shouldn't be a problem since I am storing this in a hard drive with 2.54 TB free. Could it be that by default creating a folder will not allow more than 4GB? Do you suggest any tips for checking this? Thanks! Pablo Date: Fri, 18 Sep 2015 12:06:03 -0400 From: ltirr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error downloading fs dataset Hi Pablo, Do you have enough space on your disk? It seems that it stopped downloading after 4GB of the 10.6GB file. The curl (23) error means: "Write error. Curl couldn't write data to a local filesystem or similar." Best, Lee On Fri, 18 Sep 2015, pablo najt wrote: > Dear FS experts and users, > I am coming across an error -see below, when trying to download buckner > dataset from the terminal. Any tips as to how to overcome this would be > greatly appreciated. > Thanks! > Pablo > [localhost:/Volumes/NEW_VOLUME/FS_dataset] % curl -O > ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz & > [1] 15598 > [localhost:/Volumes/NEW_VOLUME/FS_dataset] % % Total% > Received % Xferd Average Speed TimeTime Time Current >Dload Upload Total SpentLeft > Speed >37 10.6G 37 4096M0 0 2393k 0 1:17:29 0:29:12 > 0:48:17 0 > curl: (23) Failed writing body (0 != 1368) > > > > ___ 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 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 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] Error downloading fs dataset
Thanks Lee, I thought about this but this shouldn't be a problem since I am storing this in a hard drive with 2.54 TB free. Could it be that by default creating a folder will not allow more than 4GB? Do you suggest any tips for checking this? Thanks! Pablo Date: Fri, 18 Sep 2015 12:06:03 -0400 From: ltirr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error downloading fs dataset Hi Pablo, Do you have enough space on your disk? It seems that it stopped downloading after 4GB of the 10.6GB file. The curl (23) error means: "Write error. Curl couldn't write data to a local filesystem or similar." Best, Lee On Fri, 18 Sep 2015, pablo najt wrote: > Dear FS experts and users, > I am coming across an error -see below, when trying to download buckner > dataset from the terminal. Any tips as to how to overcome this would be > greatly appreciated. > Thanks! > Pablo > [localhost:/Volumes/NEW_VOLUME/FS_dataset] % curl -O > ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz & > [1] 15598 > [localhost:/Volumes/NEW_VOLUME/FS_dataset] % % Total% > Received % Xferd Average Speed TimeTime Time Current >Dload Upload Total SpentLeft > Speed >37 10.6G 37 4096M0 0 2393k 0 1:17:29 0:29:12 > 0:48:17 0 > curl: (23) Failed writing body (0 != 1368) > > > > ___ 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 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] Error downloading fs dataset
Dear FS experts and users, I am coming across an error -see below, when trying to download buckner dataset from the terminal. Any tips as to how to overcome this would be greatly appreciated. Thanks! Pablo [localhost:/Volumes/NEW_VOLUME/FS_dataset] % curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz & [1] 15598 [localhost:/Volumes/NEW_VOLUME/FS_dataset] % % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 37 10.6G 37 4096M0 0 2393k 0 1:17:29 0:29:12 0:48:17 0 curl: (23) Failed writing body (0 != 1368) ___ 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] A mixed effect model approach: Qdec possible with three group study design?
Dear Jorge, I am testing 3 groups (HC, BD, relative) and want to apply your
model. Now I am in doubt if I would be able to use qdec? Or if this instead
will not be viable as I have 3 groups is not possible with qdec?ThanksPablo
Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A mixed effect model approach in within subject
dataset
Hi Pablo
I think you can use
LME to analyze your data by ordering the rows of your design matrix
appropriately. You can consider all subjects belonging to the same
family as if they were a single subject in a longitudinal analysis.
You can put in your design matrix all subjects belonging to family1
first, then all subjects belonging to family 2 and so on. Then the
'ni' required by lme_mass_fit_vw is a vector with the number of
subjects in each family as its entries (ordered according to your
design matrix). So the length of the 'ni' vector is equal to the
number of different families in your data.
Now you can go
further and additionally order the rows of your design matrix within
each family by age. This will allow you to test the effect of age
within family.
When choosing the
random effects for your statistical model remember that a random
effect can only be the intercept term or any covariate that varies
within family. For example you can compare a model with a single
random effect for the intercept term against the same model but
considering both the intercept term and age as random effects.
Hope that helps
Cheers
-Jorge
De: pablo najt
Para: "freesurfer@nmr.mgh.harvard.edu"
Enviado: Jueves 10 de septiembre de 2015 8:07
Asunto: [Freesurfer] A mixed effect model approach in within subject dataset
Dear Freesurfer users,I wanted to enquire if anyone had successfully been able
to implement Bernal's Linear Mixed Effects (LME) Models in cross-section
dataset *not longitudinal* (please see previous thread below). I am willing to
perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates
(sex, age, and family) with "family" variable been a within-subject factor. LME
will allow to control for the non-independence of data contributed by patients
and relatives from the same families.Thanks in advance!Pablo
From: michaelnot...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 19 Feb 2014 13:10:09 +0100
Subject: [Freesurfer] Analysis of structural data acquired from multiple sites
by using a mixed effect model approach
Hi everybody,
I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls)
but have the problem that they were acquired from 4 different scanner sites. As
I can see it, there are three ways how I could tackle this problem:
1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes:
Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25
0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the
Controlls. My Problem with this approach is, that the sites don't contribute
the same amount of subjects to the analysis. I'm not sure if this could be
handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had
twice as many subjects than Site3 and Site4, I could modify the contrast to
[0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17].
2. I could create dummy variables to account for the variability between sites.
In this case, I only need to specify 3 classes (Class GroupA; Class GroupB;
Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy
variables at the end, which specify to which site a subject belongs. This
approach might work, but I'm not confident that it is the right one.
3. I could use a mixed effect model approach and specify site as a random
effect.
If I understand it correctly, the mixed effect model approach would be the best
one, as it accounts for the variability within sites. Is that correct or are
there other issues/better approaches?
I tried to implement a mixed effect model by using Bernal's Linear Mixed
Effects (LME) Models
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run
into some problems. I'm not sure if LME can only be applied on longitudinal
data or if my implementation is wrong. I have a design matrix X that specifies
the characteristics of each subject per row as follows:
Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3
Site4
1 1 0 0 11.1 99 0 0 1 0
1 0 1 0 11.1 101 0 0 1 0
1 1 0 0 11.4 95 1 0 0 0
1 0 0 1 12.4 100 1 0 0 0
...
As I have no repeated measures, 'ni' is just a vector with length X containing
'1's. If I do now the vertex-wise linear mixed-effects estimation, I get the
following output:
>> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex);
Starting m
[Freesurfer] FW: problem installing Bernal's Linear Mixed Effects (LME) Models
Hi I am reposting a previous message about difficulty to install Bernal's Linear Mixed Effects Models. I am in doubt if I should log in as a guest (I assume so). Anyway I have tried this and I get a .dmg installation file that seems to be corrupted as it does not allow me to install. Any help with be greatly appreciated. Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 10 Sep 2015 16:07:12 + Subject: Re: [Freesurfer] problem installing Bernal's Linear Mixed Effects (LME) Models Sorry Jorge to write you again,I keep getting an error when trying to install the freesurfer-Darwin-OSX-dev.dmg, "image not recognised".Do I supposed to install it from matlab?Thank,Pablo Date: Thu, 10 Sep 2015 13:44:36 + From: jbernal0...@yahoo.es To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset Hi Pablo I think you can use LME to analyze your data by ordering the rows of your design matrix appropriately. You can consider all subjects belonging to the same family as if they were a single subject in a longitudinal analysis. You can put in your design matrix all subjects belonging to family1 first, then all subjects belonging to family 2 and so on. Then the 'ni' required by lme_mass_fit_vw is a vector with the number of subjects in each family as its entries (ordered according to your design matrix). So the length of the 'ni' vector is equal to the number of different families in your data. Now you can go further and additionally order the rows of your design matrix within each family by age. This will allow you to test the effect of age within family. When choosing the random effects for your statistical model remember that a random effect can only be the intercept term or any covariate that varies within family. For example you can compare a model with a single random effect for the intercept term against the same model but considering both the intercept term and age as random effects. Hope that helps Cheers -Jorge De: pablo najt Para: "freesurfer@nmr.mgh.harvard.edu" Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model approach in within subject dataset Dear Freesurfer users,I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates (sex, age, and family) with "family" variable been a within-subject factor. LME will allow to control for the non-independence of data contributed by patients and relatives from the same families.Thanks in advance!Pablo From: michaelnot...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer] Analysis of structural data acquired from multiple sites by using a mixed effect model approach Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class GroupB; Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subj
Re: [Freesurfer] problem installing Bernal's Linear Mixed Effects (LME) Models
Sorry Jorge to write you again,I keep getting an error when trying to install the freesurfer-Darwin-OSX-dev.dmg, "image not recognised".Do I supposed to install it from matlab?Thank,Pablo Date: Thu, 10 Sep 2015 13:44:36 + From: jbernal0...@yahoo.es To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset Hi Pablo I think you can use LME to analyze your data by ordering the rows of your design matrix appropriately. You can consider all subjects belonging to the same family as if they were a single subject in a longitudinal analysis. You can put in your design matrix all subjects belonging to family1 first, then all subjects belonging to family 2 and so on. Then the 'ni' required by lme_mass_fit_vw is a vector with the number of subjects in each family as its entries (ordered according to your design matrix). So the length of the 'ni' vector is equal to the number of different families in your data. Now you can go further and additionally order the rows of your design matrix within each family by age. This will allow you to test the effect of age within family. When choosing the random effects for your statistical model remember that a random effect can only be the intercept term or any covariate that varies within family. For example you can compare a model with a single random effect for the intercept term against the same model but considering both the intercept term and age as random effects. Hope that helps Cheers -Jorge De: pablo najt Para: "freesurfer@nmr.mgh.harvard.edu" Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model approach in within subject dataset Dear Freesurfer users,I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates (sex, age, and family) with "family" variable been a within-subject factor. LME will allow to control for the non-independence of data contributed by patients and relatives from the same families.Thanks in advance!Pablo From: michaelnot...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer] Analysis of structural data acquired from multiple sites by using a mixed effect model approach Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class GroupB; Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subject per row as follows: Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3 Site4 1 1 0 0 11.1 99 0 0 1 0 1 0 1 0 11.1 101 0 0 1 0 1 1 0 0 11.4 95 1 0 0 0 1 0 0 1 12.4 100 1 0 0 0 ... As I have no repeated measures, 'ni' is just a vector with length X containing '1's. If I do now the vertex-wise linear mixed-effects estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local
Re: [Freesurfer] A mixed effect model approach in within subject dataset
Dear Jorge,Thank you very much for your generous response. I am in doubt if I
will be able to use qdec a explained in your link? Or if this instead will not
be viable as I have 3 groups?ThanksPablo
Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A mixed effect model approach in within subject
dataset
Hi Pablo
I think you can use
LME to analyze your data by ordering the rows of your design matrix
appropriately. You can consider all subjects belonging to the same
family as if they were a single subject in a longitudinal analysis.
You can put in your design matrix all subjects belonging to family1
first, then all subjects belonging to family 2 and so on. Then the
'ni' required by lme_mass_fit_vw is a vector with the number of
subjects in each family as its entries (ordered according to your
design matrix). So the length of the 'ni' vector is equal to the
number of different families in your data.
Now you can go
further and additionally order the rows of your design matrix within
each family by age. This will allow you to test the effect of age
within family.
When choosing the
random effects for your statistical model remember that a random
effect can only be the intercept term or any covariate that varies
within family. For example you can compare a model with a single
random effect for the intercept term against the same model but
considering both the intercept term and age as random effects.
Hope that helps
Cheers
-Jorge
De: pablo najt
Para: "freesurfer@nmr.mgh.harvard.edu"
Enviado: Jueves 10 de septiembre de 2015 8:07
Asunto: [Freesurfer] A mixed effect model approach in within subject dataset
Dear Freesurfer users,I wanted to enquire if anyone had successfully been able
to implement Bernal's Linear Mixed Effects (LME) Models in cross-section
dataset *not longitudinal* (please see previous thread below). I am willing to
perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates
(sex, age, and family) with "family" variable been a within-subject factor. LME
will allow to control for the non-independence of data contributed by patients
and relatives from the same families.Thanks in advance!Pablo
From: michaelnot...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 19 Feb 2014 13:10:09 +0100
Subject: [Freesurfer] Analysis of structural data acquired from multiple sites
by using a mixed effect model approach
Hi everybody,
I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls)
but have the problem that they were acquired from 4 different scanner sites. As
I can see it, there are three ways how I could tackle this problem:
1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes:
Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25
0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the
Controlls. My Problem with this approach is, that the sites don't contribute
the same amount of subjects to the analysis. I'm not sure if this could be
handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had
twice as many subjects than Site3 and Site4, I could modify the contrast to
[0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17].
2. I could create dummy variables to account for the variability between sites.
In this case, I only need to specify 3 classes (Class GroupA; Class GroupB;
Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy
variables at the end, which specify to which site a subject belongs. This
approach might work, but I'm not confident that it is the right one.
3. I could use a mixed effect model approach and specify site as a random
effect.
If I understand it correctly, the mixed effect model approach would be the best
one, as it accounts for the variability within sites. Is that correct or are
there other issues/better approaches?
I tried to implement a mixed effect model by using Bernal's Linear Mixed
Effects (LME) Models
(http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run
into some problems. I'm not sure if LME can only be applied on longitudinal
data or if my implementation is wrong. I have a design matrix X that specifies
the characteristics of each subject per row as follows:
Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3
Site4
1 1 0 0 11.1 99 0 0 1 0
1 0 1 0 11.1 101 0 0 1 0
1 1 0 0 11.4 95 1 0 0 0
1 0 0 1 12.4 100 1 0 0 0
...
As I have no repeated measures, 'ni' is just a vector with length X containing
'1's. If I do now the vertex-wise linear mixed-effects estimation, I get the
following output:
>> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex);
Starting matlabpool using the 'loca
[Freesurfer] A mixed effect model approach in within subject dataset
Dear Freesurfer users,I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates (sex, age, and family) with "family" variable been a within-subject factor. LME will allow to control for the non-independence of data contributed by patients and relatives from the same families.Thanks in advance!Pablo From: michaelnot...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer] Analysis of structural data acquired from multiple sites by using a mixed effect model approach Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class GroupB; Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subject per row as follows: Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3 Site4 1 1 0 0 11.1 99 0 0 1 0 1 0 1 0 11.1 101 0 0 1 0 1 1 0 0 11.4 95 1 0 0 0 1 0 0 1 12.4 100 1 0 0 0 ... As I have no repeated measures, 'ni' is just a vector with length X containing '1's. If I do now the vertex-wise linear mixed-effects estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local' profile ... connected to 8 workers. Starting model fitting at each location ... Location 24994: Index exceeds matrix dimensions. Location 24994: Algorithm did not converge. Initial and final likelihoods: -100, -100. Location 62484: Index exceeds matrix dimensions. Location 62484: Algorithm did not converge. Initial and final likelihoods: -100, -100. ... I've checked the matrix dimensions of X, Y, ni and lhcortex and compared them to the LME mass_univariate example stored in ADNI_Long_50sMCI_vs_50cMCI.mat but couldn't find any divergence. Has anybody encountered similar problems? Is my approach of specifying 'ni' as a vector of'1's even legitimate? Thanks, Michael ___ 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 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
[Freesurfer] Magnitude of group difference
Hello FS experts and all,I would like to find out the magnitude of the group difference between a two-group comparison (e.g. percent difference on cortical thickness indicating how much one group differs from the other.) I have run analysis using both mri_glmfit and qdec, I also run cluster wise correction for multiple comparisons but in my summary tables I am not finding this information. Do I need to run any additional command to find out about this?Thank youPablo___ 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] extract values of individual cluster
Dear FS experts,Reposting my message below.Thanks I have run two group comparison on qdec and I get differences in a number of clusters, which also survive cluster wise correction. I would like to extract the values for each of my subjects (to run further stats) on each of these clusters. Is there a way to do this rather than drawing an ROI on the clusters which will be not very precise option?Thanks in advance.Pablo ___ 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] extract values of individual cluster
Dear FS experts, I have run two group comparison on qdec and I get differences in a number of clusters, which also survive cluster wise correction. I would like to extract the values for each of my subjects (to run further stats) on each of these clusters. Is there a way to do this rather than drawing an ROI on the clusters which will be not very precise option? Thanks in advance. Pablo ___ 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] FW: Permutation output
Hi Doug,
I am attaching the permutation log file.
Thanks!
Pablo
Date: Mon, 17 Aug 2015 11:15:14 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: Permutation output
Can you send me the log file from the glmdir folder? The log file
that has "perm" in the name?
On 8/12/15 11:33 AM, pablo najt wrote:
Will do that from now on. the output is as follow:
This is the output I am getting which I believe is not what
I need for check the permutation output
C.dat F.mgh cnr.mgh gamma.mgh gammavar.mgh maxvox.dat sig.mgh
> Date: Wed, 12 Aug 2015 11:17:38 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FW: Permutation output
>
> look in the folder of one of the contrasts (eg,
> rh-Diff-BD-HC-Intercept-sulc). Also, if you can paste
such text into the
> email it is much more convenient for us than to sent us
a tiff
>
> On 08/12/2015 11:12 AM, pablo najt wrote:
> > Dear FS exp,
> > In case my message got swamped, I am reposting my
question.
> > Many thanks!
> > Pablo
> >
> >
> > From: pablon...@hotmail.com
> > To: freesurfer@nmr.mgh.harvard.edu
> > Date: Tue, 11 Aug 2015 11:02:54 +
> > Subject: Re: [Freesurfer] Permutation output
> >
> > Thanks. Sorry but I am not being able to figure it
out yet. Basically
> > I am not getting the expected outcome.
> > So I thought to give you an idea of how I am
running permutations.
> >
> > mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm
5000 1.3 perm.neg.13
> > --sim-sign neg
> >
> > And I am attaching a snapshot of the output files
and the log of
> > mdi_glmfit-sim.
> > At this stage I am wondering whether in order to
run permutation it is
> > required use as input the output from fsgd rather
than qdec, because
> > my input is from qdec. Would this make any
difference?
> > Thanks.
> > Pablo
> >
> > > Date: Mon, 10 Aug 2015 11:13:13 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Permutation output
> > >
> > > It is the same thing, but the permutation
output will have the name you
> > > gave the csdbase when you ran the simulation
(ie, the 4th arg to --sim)
> > >
> > > On 08/10/2015 05:54 AM, pablo najt wrote:
> > > > Thank you Doug.
> > > > I run permutations with mdi_glmfit-sim
--sim perm. Would you be able
> > > > to advice on the output and how to open
the permutation outputs? The
> > > > tutorial instructs on how to open the
*.summary file for the summary
> > > > of clusters and *.sig.cluster.mgh the
cluster corrected map, but not
> > > > the permutation output.
> > > > Thank you,
> > > > Pablo
> > > >
> > > >
> >
> > > > Date: Fri, 7 Aug 2015 10:53:55 -0400
> > > > From: gr...@nmr.mgh.harvard.edu
> > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > Subject: Re: [Freesurfer] Correction for
multiple comparisons - qdec
> > > >
> > > > You can try permutation, though it is
often more constraining than
> > > > those other two options. To do this,
you'll need to run
> > mri_glmfit-sim
> > > > from the command line using the --sim
perm option. Run it with --he
Re: [Freesurfer] FW: Permutation output
Will do that from now on. the output is as follow:This is the output I am getting which I believe is not what I need for check the permutation outputC.dat F.mgh cnr.mgh gamma.mgh gammavar.mghmaxvox.dat sig.mgh > Date: Wed, 12 Aug 2015 11:17:38 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: Permutation output > > look in the folder of one of the contrasts (eg, > rh-Diff-BD-HC-Intercept-sulc). Also, if you can paste such text into the > email it is much more convenient for us than to sent us a tiff > > On 08/12/2015 11:12 AM, pablo najt wrote: > > Dear FS exp, > > In case my message got swamped, I am reposting my question. > > Many thanks! > > Pablo > > > > > > From: pablon...@hotmail.com > > To: freesurfer@nmr.mgh.harvard.edu > > Date: Tue, 11 Aug 2015 11:02:54 + > > Subject: Re: [Freesurfer] Permutation output > > > > Thanks. Sorry but I am not being able to figure it out yet. Basically > > I am not getting the expected outcome. > > So I thought to give you an idea of how I am running permutations. > > > > mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 > > --sim-sign neg > > > > And I am attaching a snapshot of the output files and the log of > > mdi_glmfit-sim. > > At this stage I am wondering whether in order to run permutation it is > > required use as input the output from fsgd rather than qdec, because > > my input is from qdec. Would this make any difference? > > Thanks. > > Pablo > > > > > Date: Mon, 10 Aug 2015 11:13:13 -0400 > > > From: gr...@nmr.mgh.harvard.edu > > > To: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Permutation output > > > > > > It is the same thing, but the permutation output will have the name you > > > gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) > > > > > > On 08/10/2015 05:54 AM, pablo najt wrote: > > > > Thank you Doug. > > > > I run permutations with mdi_glmfit-sim --sim perm. Would you be able > > > > to advice on the output and how to open the permutation outputs? The > > > > tutorial instructs on how to open the *.summary file for the summary > > > > of clusters and *.sig.cluster.mgh the cluster corrected map, but not > > > > the permutation output. > > > > Thank you, > > > > Pablo > > > > > > > > > > > > > > Date: Fri, 7 Aug 2015 10:53:55 -0400 > > > > From: gr...@nmr.mgh.harvard.edu > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec > > > > > > > > You can try permutation, though it is often more constraining than > > > > those other two options. To do this, you'll need to run > > mri_glmfit-sim > > > > from the command line using the --sim perm option. Run it with --help > > > > to get examples > > > > > > > > On 8/7/15 6:59 AM, pablo najt wrote: > > > > > > > > Dear FS experts, > > > > I have a question about running corrections for multiple > > > > comparisons. I am finding a fairly large cluster analyzing 2 > > > > groups on sulcal depth. However when I tried FDR or cluster wise > > > > correction the results do not seem to survive. As the result is on > > > > the region I was predicting I want to make sure there are no other > > > > options for correcting for multiple comparisons. I am including a > > > > figure of my result to give you an idea of the size of the > > > > cluster. Do you have any suggestions for trying alternative ways > > > > of correcting? > > > > Thank you in advance, > > > > Pablo > > > > > > > > > > > > > > > > ___ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto: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.m
[Freesurfer] Permutation output
Thank you Doug.I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output.Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple comparisons. I am including a figure of my result to give you an idea of the size of the cluster. Do you have any suggestions for trying alternative ways of correcting? Thank you in advance, Pablo ___ 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.___ 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 - Generate stats data table
thanks! > Date: Tue, 4 Aug 2015 15:01:43 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qdec - Generate stats data table > > You can just run recon-all with the -wmparc flag. It should be pretty > quick, less than 30 min or soo > > On 08/04/2015 12:04 PM, pablo najt wrote: > > Thank you this subject had a zip copy of the wmparc.stats > > Now I am missing this file from another subject. Do I need to run > > recon-all from start or is there a shortcut for getting this file? > > Thanks Doug. > > Pablo > > > > > Date: Tue, 4 Aug 2015 11:42:43 -0400 > > > From: gr...@nmr.mgh.harvard.edu > > > To: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] qdec - Generate stats data table > > > > > > Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to > > > see if there might be a problem? > > > > > > On 08/04/2015 05:43 AM, pablo najt wrote: > > > > Dear FS experts, > > > > I am trying to generate my stats data tables with QDEC -after > > > > successfully loading my data table- and come across the following > > error. > > > > Any recommendations would be greatly appreciated. > > > > Thank you in advance > > > > Pablo > > > > > > > > Data table loading completed successfully. > > > > > > > > SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' > > > > > > > > mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ > > > > > > > > > > > > -- > > > > > > > > asegstats2table --common-segs --meas volume --tablefile > > > > /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat > > > > --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM > > 022LH > > > > 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC > > > > 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD > > > > 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW > > > > 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD > > > > 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON > > 456MWb > > > > 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc > > 569AG > > > > 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW > > > > 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ > > 718PJ > > > > 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG > > > > 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 > > 914JB > > > > 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG > > > > > > > > SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS > > > > > > > > Parsing the .stats files > > > > > > > > Building the table.. > > > > > > > > Writing the table to > > > > /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat > > > > > > > > > > > > -- > > > > > > > > asegstats2table --common-segs --meas volume --tablefile > > > > /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat > > > > --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM > > > > 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC > > > > 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD > > > > 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK > > > > 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW > > > > 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON > > > > 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC > > > > 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS > > 615KS > > > > 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG > > 703MHc > > > > 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM > > > > 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF > > > > 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG > > > > > > > > SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS > > > > > > > > Parsing the .stats files &g
Re: [Freesurfer] qdec - Generate stats data table
Thank you this subject had a zip copy of the wmparc.statsNow I am missing this file from another subject. Do I need to run recon-all from start or is there a shortcut for getting this file?Thanks Doug.Pablo > Date: Tue, 4 Aug 2015 11:42:43 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qdec - Generate stats data table > > Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to > see if there might be a problem? > > On 08/04/2015 05:43 AM, pablo najt wrote: > > Dear FS experts, > > I am trying to generate my stats data tables with QDEC -after > > successfully loading my data table- and come across the following error. > > Any recommendations would be greatly appreciated. > > Thank you in advance > > Pablo > > > > Data table loading completed successfully. > > > > SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' > > > > mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ > > > > > > -- > > > > asegstats2table --common-segs --meas volume --tablefile > > /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat > > --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH > > 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC > > 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD > > 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW > > 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD > > 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb > > 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG > > 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW > > 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ > > 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG > > 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB > > 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG > > > > SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS > > > > Parsing the .stats files > > > > Building the table.. > > > > Writing the table to > > /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat > > > > > > -- > > > > asegstats2table --common-segs --meas volume --tablefile > > /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat > > --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM > > 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC > > 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD > > 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK > > 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW > > 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON > > 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC > > 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS > > 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc > > 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM > > 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF > > 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG > > > > SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS > > > > Parsing the .stats files > > > > ERROR: The stats file /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats > > is not found or is too small to be a valid statsfile > > > > Use --skip flag to automatically skip bad stats files > > > > > > > > ___ > > 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 b
[Freesurfer] qdec - Generate stats data table
Dear FS experts,I am trying to generate my stats data tables with QDEC -after successfully loading my data table- and come across the following error.Any recommendations would be greatly appreciated.Thank you in advancePabloData table loading completed successfully. SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files Building the table.. Writing the table to /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files ERROR: The stats file /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ___ 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] 3 Group comparison
Dear Doug,Thank you very much for your response. I am attaching my g3vo.txt file -have changed extension now.I finally manage to make it work but I am not confident if this is the ideal way of running a design for 3 groups 1 factor 3 levels no covariates as FS indicate (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V). This is how I am running it: mri_glmfit --glmdir rh.thickness.g3v0.glmdir --y rh.g3v0.thickness.15B.mgh --fsgd g3v0.txt --C HC-BD_fam.mtx --C HC-BD.mtx --C BD-BD_fam.mtx --C group.effect.mtx --C HC+BD-vs-BD_fam.mtx --surf fsaverage rh --cortex And run separately for volume and white.But my question is should I be running it using y.mgh instead (as below)? mri_glmfit \ --glmdir g3v0 \ --y y.mgh \ --fsgd g3v0.fsgd \ --C normal-mci.mtx \ --C normal-ad.mtx \ --C mci-ad.mtx \ --C group.effect.mtx \ --C normal+mci-vs-ad.mtxBut my problem is that I would need to run in Qdec and this is not for more than 2 group analyses?Many thanks!Pablo > Date: Wed, 8 Jul 2015 17:35:21 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 3 Group comparison > > There is not a --meas option for mri_glmfit, you need to give it a --y > option explicity, though it may be trying to read a yfile if you have > one in the FSGD. How did you make g3v0.fsgd? Can you send it? The second > command looks like you are doing the right thing, you just need to tell > mri_glmfit that this is surface data by adding --surface fsaverage hemi > > where hemi is lh or rh > > doug > > On 07/07/2015 06:45 AM, pablo najt wrote: > > Dear FS experts, > > I am trying to run a 3 group comparison with FS. > > I have run preproc ( script from ENIGMA Cortical protocol) on my first > > fsgd file. > > > > As I have three groups I have prepared my second fsgd file as g3v0.fsgd > > and all my desired contrasts, rather than using QDEC. > > > > I run this second stage as follows: > > mri_glmfit \ > > --glmdir g3v0 \ > > --meas thickness ../SURF/lh.thickness.mgh \ > > --fsgd g3v0.fsgd \ > > --C HC-BD_fam.mtx \ > > --C HC-BD.mtx \ > > --C BD-BD_fam.mtx \ > > --C group.effect.mtx \ > > --C HC+BD-vs-BD_fam.mtx > > > > and I get: > > > > Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh > > > > mghRead(/Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh, -1): could > > not open file > > > > ERROR: loading y /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh > > > > > > As far as I understand y.mgh is a stack data that is made after using > > QDEC is run. But I have been prompted to not use QDEC, so I am now > > wondering how I am supposed to run my glm design. > > > > Also I tried to change the y.mgh to any of the outputs of the > > mris_preproc (lh.white.mgh, lh.volume.mgh, lh.thickness.mgh, etc), and > > it says: > > > > Creating output directory g3v0 > > > > Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/SURF/rh.white.mgh > > > > ERROR: you must use '--surface subject hemi' with surface data > > > > Any suggestion would be greatly appreciated. > > Thanks a lot. > > Pablo > > > > > > ___ > > 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. > GroupDescriptorFile 1 Title OSGM Class HC Class BD Class BD-Fam Input 001ER BD Input 011GB BD Input 018AM HC Input 045PC BD-Fam Input 054JB HC Input 058CS BD Input 062AH BD-Fam
[Freesurfer] 3 group comparison
Dear FS experts following to my query below I run into further errors. If anyone could advice it would be great help.Regards,Pablomri_glmfit \ --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods\ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdir? --y lh.g3v0.thickness.10B.mgh \? --fsgd g3v0.fsgd dods\? --C HC-BD_fam.mtx \ gdfReadHeader: reading g3v0.fsgdINFO: gd2mtx_method is dodsERROR: must specify GLM output dir[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% --surf fsaverage lh \? --cortex \? --glmdir lh.g3v0.glmdir--surf: Command not found.[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% mri_glmfit \ --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods \ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdir? --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods \ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdirERROR: Option --fsgd unknown[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% [pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% mri_glmfit \ --glmdir g3v0 \ --y h.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd \ --C HC-BD_fam.mtx \ --C HC-BD.mtx \ --C BD-BD_fam.mtx \ --C group.effect.mtx \ --C HC+BD-vs-BD_fam.mtxERROR: Option --glmdir unknown[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% mri_glmfit \ --glmdir g3v0 \ --y y.mgh \ --fsgd g3v0.fsgd \ --C HC-BD_fam.mtx \ --C HC-BD.mtx \ --C BD-BD_fam.mtx \ --C group.effect.mtx \ --C HC+BD-vs-BD_fam.mtxERROR: Option --glmdir unknown[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% Previous message begin here--Dear FS experts, I am trying to run a 3 group comparison with FS.I have run preproc ( script from ENIGMA Cortical protocol) on my first fsgd file. As I have three groups I have prepared my second fsgd file as g3v0.fsgd and all my desired contrasts, rather than using QDEC. I run this second stage as follows:mri_glmfit \ --glmdir g3v0 \ --meas thickness ../SURF/lh.thickness.mgh \ --fsgd g3v0.fsgd \ --C HC-BD_fam.mtx \ --C HC-BD.mtx \ --C BD-BD_fam.mtx \ --C group.effect.mtx \ --C HC+BD-vs-BD_fam.mtx and I get:Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mghmghRead(/Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh, -1): could not open fileERROR: loading y /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh As far as I understand y.mgh is a stack data that is made after using QDEC is run. But I have been prompted to not use QDEC, so I am now wondering how I am supposed to run my glm design. Also I tried to change the y.mgh to any of the outputs of the mris_preproc (lh.white.mgh, lh.volume.mgh, lh.thickness.mgh, etc), and it says:Creating output directory g3v0Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/SURF/rh.white.mghERROR: you must use '--surface subject hemi' with surface dataAny suggestion would be greatly appreciated.Thanks a lot.Pablo___ 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 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] 3 Group comparison
Dear FS experts,I am trying to run a 3 group comparison with FS.I have run preproc ( script from ENIGMA Cortical protocol) on my first fsgd file. As I have three groups I have prepared my second fsgd file as g3v0.fsgd and all my desired contrasts, rather than using QDEC. I run this second stage as follows:mri_glmfit \ --glmdir g3v0 \ --meas thickness ../SURF/lh.thickness.mgh \ --fsgd g3v0.fsgd \ --C HC-BD_fam.mtx \ --C HC-BD.mtx \ --C BD-BD_fam.mtx \ --C group.effect.mtx \ --C HC+BD-vs-BD_fam.mtx and I get:Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mghmghRead(/Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh, -1): could not open fileERROR: loading y /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh As far as I understand y.mgh is a stack data that is made after using QDEC is run. But I have been prompted to not use QDEC, so I am now wondering how I am supposed to run my glm design. Also I tried to change the y.mgh to any of the outputs of the mris_preproc (lh.white.mgh, lh.volume.mgh, lh.thickness.mgh, etc), and it says:Creating output directory g3v0Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/SURF/rh.white.mghERROR: you must use '--surface subject hemi' with surface dataAny suggestion would be greatly appreciated.Thanks a lot.Pablo ___ 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] FW: Error #@# MotionCor {Disarmed}
Thanks Pablo Date: Sat, 9 May 2015 15:58:19 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Error #@# MotionCor Hi Pablo why are you listing fsaverage as the subject you are processing? The error says you are runing: recon-all -s fsaverage which is not what you want. cheers Bruce On Sat, 9 May 2015, pablo najt wrote: > Hello I guess my message got lost in the long mailing list. If anyone is > able to advice on the message I will be grateful to you. > Thanks > Pablo > > > From: pablon...@hotmail.com > To: freesurfer@nmr.mgh.harvard.edu > Date: Thu, 7 May 2015 16:37:29 + > Subject: [Freesurfer] Error #@# MotionCor > > Dear FS experts, > I am processing my subjects with a foreach batch as below. > > foreach I (*) > echo $i > recon-all -subjd $i -all > end > > I run this in four parallel terminals and save output in 4 different > folders. Once they are finshed I moved all output to a main output folder > and process a new batch of subjects. > > The recon-all.log reads "finished without error" but at the end of each of > the batches I get the following error. Should I'll be warring about this? > For further reference I am attaching the recon-all.log file. But as I said I > cannot find anything wrong with it. > Thanks, > Pablo > > # > #@# MotionCor Sat May 2 07:48:28 IST 2015 > ERROR: no run data found in > /media/OS/ENIGMA_Genetic_Risk/output_batch4/fsaverage/mri. Make sure to > have a volume called 001.mgz in > /media/OS/ENIGMA_Genetic_Risk/output_batch4/fsaverage/mri/orig. > If you have a second run of data call it 002.mgz, etc. > See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > Linux dara-Precision 3.0.0-21-generic #35-Ubuntu SMP Fri May 25 17:57:41 UTC > 2012 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s fsaverage exited with ERRORS at Sat May 2 07:48:28 IST 2015 > > For more details, see the log > file/media/OS/ENIGMA_Genetic_Risk/output_batch4/fsaverage/scripts/recon-all.log > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > lh.EC_average > ERROR: you do not have write permission to > /media/OS/ENIGMA_Genetic_Risk/output_batch4/lh.EC_average > rh.EC_average > ERROR: you do not have write permission to > /media/OS/ENIGMA_Genetic_Risk/output_batch4/rh.EC_average > dara-Precision:/media/OS/ENIGMA_Genetic_Risk/output_batch4> > > > > > ___ 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 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 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] Batch processing
Dear FS experts, I am trying to run recon-all -i plus recon-all -all in a for loop to run trough 250 subjects as efficient as possible. I am using OSX any suggestions from previous cases? Thank you for your help, Pablo ___ 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] Analyze format
Thank you Bruce for the piece of mind. The images were neurologically oriented (L=L) for analysis with SPM. Do you know if this helps at all? Thanks Pablo Date: Wed, 25 Feb 2015 10:44:48 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Analyze format Hi Pablo the mat file is an extension to analyze the specifies the direction cosines. Without it we are only guessing at the anatomical orientation of the image. Unless these images have some marker such as a vitamin E capsule how will you ever know if we got left/right correct? cheers Bruce On Wed, 25 Feb 2015, pablo najt wrote: > Dear FS experts,I am trying to run recon-all on data with analyze format. I > am aware that this is not the best format, however I do not have DICOM or > NIFTI original data as this is a very old data from University of North > Carolina. > > When I run import the images with recon-all -i. I am getting the following > log below. Do you advice to proceed with recon-all -all or do you there is a > way I could obtain the mat file that freesurfer is asking? > Thank you > Pablo > recon-all -i 30225.img -s 30225 > > >mri_convert /home/0116442s/FS_test/30225.img > /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz > > mri_convert /home/0116442s/FS_test/30225.img > /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz > - > INFO: could not find /home/0116442s/FS_test/30225.mat file for > direction cosine info. > INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. > INFO: if not valid, please provide the information in > /home/0116442s/FS_test/30225.mat file > - > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /home/0116442s/FS_test/30225.img... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, 1) > k_ras = (0, 1, 0) > writing to /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz... > > #-- > > recon-all -s 30225 finished without error at Wed Feb 25 15:30:09 GMT > 2015 > done > > > > ___ 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 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] Analyze format
Dear FS experts,I am trying to run recon-all on data with analyze format. I am aware that this is not the best format, however I do not have DICOM or NIFTI original data as this is a very old data from University of North Carolina. When I run import the images with recon-all -i. I am getting the following log below. Do you advice to proceed with recon-all -all or do you there is a way I could obtain the mat file that freesurfer is asking?Thank youPablorecon-all -i 30225.img -s 30225 mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz mri_convert /home/0116442s/FS_test/30225.img /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz -INFO: could not find /home/0116442s/FS_test/30225.mat file for direction cosine info.INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped.INFO: if not valid, please provide the information in /home/0116442s/FS_test/30225.mat file-$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /home/0116442s/FS_test/30225.img...TR=0.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, 0)j_ras = (0, 0, 1)k_ras = (0, 1, 0)writing to /home/0116442s/FS_test/SURF/30225/mri/orig/001.mgz... #-- recon-all -s 30225 finished without error at Wed Feb 25 15:30:09 GMT 2015done ___ 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] Strange background when opening brain mask
FreeSurfer experts,I have a question about one of my scans after running recon-all -all. When I open the image with freeview for inspecting brain mask volume.To give you a better idea of the problem I have attached a screenshot of the T1 volume. All my other images did not show the coloured black background that observed here, so I am wondering what might be the problem.To open T1 I have used the suggested command:freeview -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=redMy scans have been processed in nifti format. Also I have previously run nu_correct for correction of artefacts in the top of the brain.I also opened this particular scan and it looks very similar to the others.Thank you in advance for your attention.Pablo ___ 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] Output of recon-all -all -openmp 8 does not show brainmask.mgz
Dear Zeke,I am forwarding the email below that I believe it got lost in the dense list of correspondences.I would highly appreciate your input.Thanks,Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 19 Dec 2013 15:27:11 + Subject: Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz Dear Zeke, Thank you for pointing in the right direction. As a reminder the problem was that I was not getting the brainmask.mgz file, in the meantime I tried to re run finally got it . \ However, I am surprised of the duration of recon-all -all -openmp 8 (using a linux workstation with 8 cores (2 processors with 4 each). Running 5 subjects simultaneously took up to 52 hours. 4 subjects around 40 hours. Any way I am attaching the recon-all.log file just to be sure that there are no strange errors. Thank you so much, Pablo > Date: Mon, 16 Dec 2013 17:18:32 -0500 > From: zkauf...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu; pablon...@hotmail.com > Subject: Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show > brainmask.mgz > > Pablo, > > I need the recon-all.log file located in the $SUBJECTS_DIR/scripts > directory. Sorry for the confusion. > > -Zeke > > On 12/13/2013 04:48 PM, pablo najt wrote: > > Dear Zeke, > > Thank you so much. As I am not sure which is the log file that we use I > > am attaching mri_nu (in mri directory) and talairach_avi (in > > mri/transformations directory). > > Thanks, > > Pablo > > > > > Date: Fri, 13 Dec 2013 16:21:48 -0500 > > > From: zkauf...@nmr.mgh.harvard.edu > > > To: pablon...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Output of recon-all -all -openmp 8 does not > > show brainmask.mgz > > > > > > Hello Pablo, > > > > > > Please send me the recon-all.log file for the subject and I will take a > > > look. > > > > > > -Zeke > > > > > > On 12/13/2013 03:41 PM, pablo najt wrote: > > > > Dear FS, > > > > I am checking on the outputs of recon-all -all using the flag > > -openmp 8. > > > > As I did with standard recon-all -all comand line I was trying to check > > > > brainmask.mgz, but there is not such file. Is there anything wrong with > > > > my outputs? Or I should be checking a different file? > > > > Thank you, > > > > Pablo > > > > > > > > > > > > ___ > > > > 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 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 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] Output of recon-all -all -openmp 8 does not show brainmask.mgz
Dear FS, I am checking on the outputs of recon-all -all using the flag -openmp 8. As I did with standard recon-all -all comand line I was trying to check brainmask.mgz, but there is not such file. Is there anything wrong with my outputs? Or I should be checking a different file? Thank you, Pablo ___ 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] FW: -openmp 8 flag for recon-all
Dear FS experts, I have the following questions that I am thinking probably got lost in the list of emails. I would be grateful if you can help me out. Please find the questions below. Many thanks, Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 11 Dec 2013 15:12:09 + Subject: [Freesurfer] -openmp 8 flag for recon-all Dear Bruce and FS experts,I am running recon-all using the longitudinal stream. I have a question regarding the specific command line for recon-all using the -openmp flag and regarding the organizing directory of longitudinal data. I am using FS version 5.3 CentOS 6 and in a linux work station with two processors with 4 cores (8 cores total).As far as I understand I can use the openmp 8 flag. But I just wanted to confirm the exact command line would be [recon -all -s -openmp 8] ?Also, do I need to include this flag for importing the files: [e.g. recon-all -i ... -s -openmp 8 ...] One last query, is there any command lines for organizing the subjects in terms of time point 1 and time point 2 for each subject?Thank you,Pablo > > Date: Tue, 26 Nov 2013 16:41:31 -0500 > > From: fis...@nmr.mgh.harvard.edu > > To: pablon...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > Hi Pablo > > > > it also depends on how much ram it has. You should be able to run 1 > > significantly faster using the -openmp 8 flag to recon-all, or 8 (if you > > have enough ram, probably at least 32G) > > > > cheers > > Bruce > > > > On Tue, 26 Nov 2013, pablo najt > > wrote: > > > > > Dear Bruce,Last week I emailed with the question of how many recon -all > > > separate subjects I could run in parallel with the FS version 5.3 for Cent > > os > > > 6. You answered that this depends on how many cores my machine has. > > > I just found out that our workstation has two processors with 4 cores each > > > (8 cores in total). > > > Would you be able to tell me how many subjects could I run in parallel wit > > h > > > our workstation? > > > Thank you for your support, > > > Pablo > > > > > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > > > From: fis...@nmr.mgh.harvard.edu > > > To: pablon...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > > > Hi Pablo > > > > > > it depends on how many cores you have > > > > > > Bruce > > > On Thu, 21 Nov 2013, pablo najt wrote: > > > > > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I > > a > > > m > > > > wondering up to how many recon -all for separate subjects I can run in > > > > parallel. With the version of Snow Leopard 32b I was running two at a ti > > me > > > > and it took around 20 hours. Would I be able to run 6 subjects in parall > > el > > > ? > > > > If so would this process still efficient or there is an optimum number? > > > > Thank you, > > > > Pablo > > > > > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > > > From: zkauf...@nmr.mgh.harvard.edu > > > > > To: gariko...@gmail.com > > > > > CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > > > CentOS 6 > > > > > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > > > CentOS6 build. > > > > > > > > > > -Zeke > > > > > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in a > > ny > > > > > > reason to not use this version in your CentOS 6, if you have some ot > > he > > > r > > > > > > requirements maybe Nick or Zeke could help you better, I am just an > > us > > > er > > > > :) > > > > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt > > > > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > > > > > > > Dear Gari, > > > > > > Thank you for the advice. One additional question. > > > > > > Considering that I will start from scratch the pr
[Freesurfer] -openmp 8 flag for recon-all
Dear Bruce and FS experts,I am running recon-all using the longitudinal stream. I have a question regarding the specific command line for recon-all using the -openmp flag and regarding the organizing directory of longitudinal data. I am using FS version 5.3 CentOS 6 and in a linux work station with two processors with 4 cores (8 cores total).As far as I understand I can use the openmp 8 flag. But I just wanted to confirm the exact command line would be [recon -all -s -openmp 8] ?Also, do I need to include this flag for importing the files: [e.g. recon-all -i ... -s -openmp 8 ...] One last query, is there any command lines for organizing the subjects in terms of time point 1 and time point 2 for each subject?Thank you,Pablo > > Date: Tue, 26 Nov 2013 16:41:31 -0500 > > From: fis...@nmr.mgh.harvard.edu > > To: pablon...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > Hi Pablo > > > > it also depends on how much ram it has. You should be able to run 1 > > significantly faster using the -openmp 8 flag to recon-all, or 8 (if you > > have enough ram, probably at least 32G) > > > > cheers > > Bruce > > > > On Tue, 26 Nov 2013, pablo najt > > wrote: > > > > > Dear Bruce,Last week I emailed with the question of how many recon -all > > > separate subjects I could run in parallel with the FS version 5.3 for Cent > > os > > > 6. You answered that this depends on how many cores my machine has. > > > I just found out that our workstation has two processors with 4 cores each > > > (8 cores in total). > > > Would you be able to tell me how many subjects could I run in parallel wit > > h > > > our workstation? > > > Thank you for your support, > > > Pablo > > > > > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > > > From: fis...@nmr.mgh.harvard.edu > > > To: pablon...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > > > Hi Pablo > > > > > > it depends on how many cores you have > > > > > > Bruce > > > On Thu, 21 Nov 2013, pablo najt wrote: > > > > > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I > > a > > > m > > > > wondering up to how many recon -all for separate subjects I can run in > > > > parallel. With the version of Snow Leopard 32b I was running two at a ti > > me > > > > and it took around 20 hours. Would I be able to run 6 subjects in parall > > el > > > ? > > > > If so would this process still efficient or there is an optimum number? > > > > Thank you, > > > > Pablo > > > > > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > > > From: zkauf...@nmr.mgh.harvard.edu > > > > > To: gariko...@gmail.com > > > > > CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > > > CentOS 6 > > > > > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > > > CentOS6 build. > > > > > > > > > > -Zeke > > > > > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in a > > ny > > > > > > reason to not use this version in your CentOS 6, if you have some ot > > he > > > r > > > > > > requirements maybe Nick or Zeke could help you better, I am just an > > us > > > er > > > > :) > > > > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt > > > > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > > > > > > > Dear Gari, > > > > > > Thank you for the advice. One additional question. > > > > > > Considering that I will start from scratch the processing in the > > > > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > > > > Thanks, > > > > > > Pablo > > > > > > > > > > > > > > -- > > > -- > > > > > >
[Freesurfer] FW: recon -all in FS version 5.3 CentOS 6
Dear FS experts,I am forwarding a message I sent yesterday that my got lost in the long list of email. My question is as follow: As far as I understood the FS version for Mac snow Leopard is not compatible with FS version 5.3 CentOS 6 (see response I got below). Is this correct or I could combine subjects processed with i386 and CentOS 6 releases? Pablo From: garikoitz@gmail.comDate: Wed, 20 Nov 2013 18:23:40 +0100Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6To: pablonajt@hotmail.comCC: freesurfer@nmr.mgh.harvard.edu > > > > > > Hi Pablo, > > > > > > you shouldn't mix different OS-s or software version in the same > > > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > > > operating system version on anatomical volume and cortical thickness > > > > > > measurements. /PloS one/, /7/(6), e38234. > > > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > > > it works too). > > > > > > regards! > > > > > > Gari > > > > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt > > > > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > > > > > > > Dear FS experts, > > > > > > I am forwarding my question (please see below), in case it got > > > > > > lost among the intense flow of messages. > > > > > > Thank you for your consideration. > > > > > > Pablo > > > > > > > > > > > > > > -- > > > -- > > > > > > From: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > > Date: Mon, 18 Nov 2013 16:38:41 + > > > > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > > and CentOS 6 > > > > > > > > > > > > > > > > > > Dear FS experts, > > > > > > I have a question about compatibility for running recon-all > > > > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > > > > > > > I already run recon all- for several of my subjects with a Mac > > > > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > > > > access to an additional machine (a linux CentOS 6 (64b)) I was > > > > > > wondering if I could process additional subjects in parallel > > > > > > with this other machine that are also intended to be included in > > > > > > the longitudinal stream. > > > > > > Also, I am not sure about whether I should be installing in the > > > > > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > > > > > because of compatibility issues. > > > > > > Thank you very much for your attention, > > > > > > Pablo > > > > > > > > > > > > > > > > > > ___ Freesurfer > > > > > > mailing list Freesurfer@nmr.mgh.harvard.edu > > > > > > <mailto: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] recon -all in FS version 5.3 CentOS 6
Hello Bruce,As far as I understood the FS version for Mac snow Leopard is not compatible with FS version 5.3 CentOS 6 (see response I got below). Is this correct or I could combine subjects processed with i386 and CentOS 6 releases? Pablo From: garikoitz@gmail.comDate: Wed, 20 Nov 2013 18:23:40 +0100Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6To: pablonajt@hotmail.comCC: freesurfer@nmr.mgh.harvard.edu > > > > > > Hi Pablo, > > > > > > you shouldn't mix different OS-s or software version in the same > > > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > > > operating system version on anatomical volume and cortical thickness > > > > > > measurements. /PloS one/, /7/(6), e38234. > > > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > > > it works too). > > > > > > regards! > > > > > > Gari > > > > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt > > > > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > > > > > > > Dear FS experts, > > > > > > I am forwarding my question (please see below), in case it got > > > > > > lost among the intense flow of messages. > > > > > > Thank you for your consideration. > > > > > > Pablo > > > > > > > > > > > > > > -- > > > -- > > > > > > From: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > > Date: Mon, 18 Nov 2013 16:38:41 + > > > > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > > and CentOS 6 > > > > > > > > > > > > > > > > > > Dear FS experts, > > > > > > I have a question about compatibility for running recon-all > > > > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > > > > > > > I already run recon all- for several of my subjects with a Mac > > > > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > > > > access to an additional machine (a linux CentOS 6 (64b)) I was > > > > > > wondering if I could process additional subjects in parallel > > > > > > with this other machine that are also intended to be included in > > > > > > the longitudinal stream. > > > > > > Also, I am not sure about whether I should be installing in the > > > > > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > > > > > because of compatibility issues. > > > > > > Thank you very much for your attention, > > > > > > Pablo > > > > > > > > > > > > > > > > > > ___ Freesurfer > > > > > > mailing list Freesurfer@nmr.mgh.harvard.edu > > > > > > <mailto: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.
Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
Thank you Bruce for your reply.Yes the computed has over 32 GB. Let me check if I understood.So far I have been running recon -all in a snow leopard for running as part of the longitudinal stream.If I want to re-start with this analysis in the FS 5.3 version for Centos you are suggesting I can use the a new recon -all command (-openmp 8 flag to recon-all)? Thanks.Pablo Date: Tue, 26 Nov 2013 16:41:31 -0500 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 Hi Pablo it also depends on how much ram it has. You should be able to run 1 significantly faster using the -openmp 8 flag to recon-all, or 8 (if you have enough ram, probably at least 32G) cheers Bruce On Tue, 26 Nov 2013, pablo najt wrote: > Dear Bruce,Last week I emailed with the question of how many recon -all > separate subjects I could run in parallel with the FS version 5.3 for Centos > 6. You answered that this depends on how many cores my machine has. > I just found out that our workstation has two processors with 4 cores each > (8 cores in total). > Would you be able to tell me how many subjects could I run in parallel with > our workstation? > Thank you for your support, > Pablo > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > From: fis...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > Hi Pablo > > it depends on how many cores you have > > Bruce > On Thu, 21 Nov 2013, pablo najt wrote: > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I a > m > > wondering up to how many recon -all for separate subjects I can run in > > parallel. With the version of Snow Leopard 32b I was running two at a time > > and it took around 20 hours. Would I be able to run 6 subjects in parallel > ? > > If so would this process still efficient or there is an optimum number? > > Thank you, > > Pablo > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > From: zkauf...@nmr.mgh.harvard.edu > > > To: gariko...@gmail.com > > > CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > CentOS 6 > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > CentOS6 build. > > > > > > -Zeke > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any > > > > reason to not use this version in your CentOS 6, if you have some othe > r > > > > requirements maybe Nick or Zeke could help you better, I am just an us > er > > :) > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt > > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > > > Dear Gari, > > > > Thank you for the advice. One additional question. > > > > Considering that I will start from scratch the processing in the > > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > > Thanks, > > > > Pablo > > > > > > > > -- > -- > > > > From: gariko...@gmail.com <mailto:gariko...@gmail.com> > > > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > > > To: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > and CentOS 6 > > > > > > > > > > > > Hi Pablo, > > > > you shouldn't mix different OS-s or software version in the same > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > operating system version on anatomical volume and cortical thickness > > > > measurements. /PloS one/, /7/(6), e38234. > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > it works too). > > > > regards! > > > > Gari > > > > > > > > > >
Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
Dear Bruce,Last week I emailed with the question of how many recon -all separate subjects I could run in parallel with the FS version 5.3 for Centos 6. You answered that this depends on how many cores my machine has. I just found out that our workstation has two processors with 4 cores each (8 cores in total).Would you be able to tell me how many subjects could I run in parallel with our workstation?Thank you for your support,Pablo Date: Thu, 21 Nov 2013 10:47:34 -0500 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 Hi Pablo it depends on how many cores you have Bruce On Thu, 21 Nov 2013, pablo najt wrote: > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am > wondering up to how many recon -all for separate subjects I can run in > parallel. With the version of Snow Leopard 32b I was running two at a time > and it took around 20 hours. Would I be able to run 6 subjects in parallel? > If so would this process still efficient or there is an optimum number? > Thank you, > Pablo > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > From: zkauf...@nmr.mgh.harvard.edu > > To: gariko...@gmail.com > > CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > CentOS 6 > > > > I have to agree with Gari, I see no reason for you to not use the > > CentOS6 build. > > > > -Zeke > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any > > > reason to not use this version in your CentOS 6, if you have some other > > > requirements maybe Nick or Zeke could help you better, I am just an user > :) > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > Dear Gari, > > > Thank you for the advice. One additional question. > > > Considering that I will start from scratch the processing in the > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > Thanks, > > > Pablo > > > > > > > > > From: gariko...@gmail.com <mailto:gariko...@gmail.com> > > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > > To: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > > CC: freesurfer@nmr.mgh.harvard.edu > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > and CentOS 6 > > > > > > > > > Hi Pablo, > > > you shouldn't mix different OS-s or software version in the same > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > effects of FreeSurfer version, workstation type, and Macintosh > > > operating system version on anatomical volume and cortical thickness > > > measurements. /PloS one/, /7/(6), e38234. > > > doi:10.1371/journal.pone.0038234). > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > it works too). > > > regards! > > > Gari > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > Dear FS experts, > > > I am forwarding my question (please see below), in case it got > > > lost among the intense flow of messages. > > > Thank you for your consideration. > > > Pablo > > > > > > > > > From: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > > To: freesurfer@nmr.mgh.harvard.edu > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Date: Mon, 18 Nov 2013 16:38:41 + > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > and CentOS 6 > > > > > > > > > Dear FS experts, > > > I have a question about compatibility for running recon-all > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > I already run recon all- for several of my subjects with a Mac > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > access to an
[Freesurfer] recon -all in FS version 5.3 CentOS 6
Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am wondering up to how many recon -all for separate subjects I can run in parallel. With the version of Snow Leopard 32b I was running two at a time and it took around 20 hours. Would I be able to run 6 subjects in parallel? If so would this process still efficient or there is an optimum number?Thank you,Pablo > Date: Wed, 20 Nov 2013 13:11:15 -0500 > From: zkauf...@nmr.mgh.harvard.edu > To: gariko...@gmail.com > CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 > > I have to agree with Gari, I see no reason for you to not use the > CentOS6 build. > > -Zeke > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any > > reason to not use this version in your CentOS 6, if you have some other > > requirements maybe Nick or Zeke could help you better, I am just an user :) > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt > <mailto:pablon...@hotmail.com>> wrote: > > > > Dear Gari, > > Thank you for the advice. One additional question. > > Considering that I will start from scratch the processing in the > > CentOS 6, which would be the recommended FS version for CentOS 6? > > Thanks, > > Pablo > > > > > > From: gariko...@gmail.com <mailto:gariko...@gmail.com> > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > To: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > CC: freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > and CentOS 6 > > > > > > Hi Pablo, > > you shouldn't mix different OS-s or software version in the same > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > effects of FreeSurfer version, workstation type, and Macintosh > > operating system version on anatomical volume and cortical thickness > > measurements. /PloS one/, /7/(6), e38234. > > doi:10.1371/journal.pone.0038234). > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > it works too). > > regards! > > Gari > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt > <mailto:pablon...@hotmail.com>> wrote: > > > > Dear FS experts, > > I am forwarding my question (please see below), in case it got > > lost among the intense flow of messages. > > Thank you for your consideration. > > Pablo > > > > > > > > From: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > To: freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Date: Mon, 18 Nov 2013 16:38:41 + > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > and CentOS 6 > > > > > > Dear FS experts, > > I have a question about compatibility for running recon-all > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > SnowLeopard OS X 10.6 (32b Intel). > > > > I already run recon all- for several of my subjects with a Mac > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > access to an additional machine (a linux CentOS 6 (64b)) I was > > wondering if I could process additional subjects in parallel > > with this other machine that are also intended to be included in > > the longitudinal stream. > > Also, I am not sure about whether I should be installing in the > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > because of compatibility issues. > > Thank you very much for your attention, > > Pablo > > > > > > ___ Freesurfer > > mailing list Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The > > information in this
Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Thanks,Pablo > Date: Wed, 20 Nov 2013 13:11:15 -0500 > From: zkauf...@nmr.mgh.harvard.edu > To: gariko...@gmail.com > CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 > > I have to agree with Gari, I see no reason for you to not use the > CentOS6 build. > > -Zeke > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any > > reason to not use this version in your CentOS 6, if you have some other > > requirements maybe Nick or Zeke could help you better, I am just an user :) > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt > <mailto:pablon...@hotmail.com>> wrote: > > > > Dear Gari, > > Thank you for the advice. One additional question. > > Considering that I will start from scratch the processing in the > > CentOS 6, which would be the recommended FS version for CentOS 6? > > Thanks, > > Pablo > > > > > > From: gariko...@gmail.com <mailto:gariko...@gmail.com> > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > To: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > CC: freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > and CentOS 6 > > > > > > Hi Pablo, > > you shouldn't mix different OS-s or software version in the same > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > effects of FreeSurfer version, workstation type, and Macintosh > > operating system version on anatomical volume and cortical thickness > > measurements. /PloS one/, /7/(6), e38234. > > doi:10.1371/journal.pone.0038234). > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > it works too). > > regards! > > Gari > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt > <mailto:pablon...@hotmail.com>> wrote: > > > > Dear FS experts, > > I am forwarding my question (please see below), in case it got > > lost among the intense flow of messages. > > Thank you for your consideration. > > Pablo > > > > > > > > From: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > To: freesurfer@nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Date: Mon, 18 Nov 2013 16:38:41 + > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > and CentOS 6 > > > > > > Dear FS experts, > > I have a question about compatibility for running recon-all > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > SnowLeopard OS X 10.6 (32b Intel). > > > > I already run recon all- for several of my subjects with a Mac > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > access to an additional machine (a linux CentOS 6 (64b)) I was > > wondering if I could process additional subjects in parallel > > with this other machine that are also intended to be included in > > the longitudinal stream. > > Also, I am not sure about whether I should be installing in the > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > because of compatibility issues. > > Thank you very much for your attention, > > Pablo > > > > > > ___ Freesurfer > > mailing list Freesurfer@nmr.mgh.harvard.edu > > <mailto: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 e
Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear Gari,Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6?Thanks,Pablo From: gariko...@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo,you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. PloS one, 7(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too).regards!Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt wrote: Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention,Pablo ___ 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 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 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 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] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues.Thank you very much for your attention,Pablo ___ 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 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] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues.Thank you very much for your attention,Pablo ___ 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] FW: No brain tissue after recon-all all
Thank you. One more question, is there any way to check if this affect the surfaces after running recon-all -all?Or I need to complete the whole analysis before looking into this?Cheers,Pablo > Date: Tue, 3 Sep 2013 11:07:36 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: No brain tissue after recon-all all > > > Yes, that is just some eyeball that has not been stripped. It is ok as > long as it does not affect the surfaces. > doug > > > On 09/03/2013 10:54 AM, pablo najt wrote: > > Hi Doug, > > Thank you very much for your output about my output files. Yes, I > > understand that these images are skull stripped. But since there are > > possibilities of error in the skull stripping process I was concern > > about extra no brain tissue being included in the output. > > > > I think the location of the tissue I was referring was mistaken. To > > make it clearer I have circled (in red) the specific area in the > > images attached I have concerns about not being brain tissue. > > > > I noticed that this repeats in several other of my subjects and I > > wanted to make sure it is fine. > > > > Best, > > Pablo > > > > > > > Date: Tue, 3 Sep 2013 09:50:06 -0400 > > > From: gr...@nmr.mgh.harvard.edu > > > To: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] No brain tissue after recon-all all > > > > > > > > > Hi Pablo, this is a skull stripped image. In the human brain there > > is no > > > brain tissue ventral to the orbital frontal areaso any tissue there has > > > been stripped away. > > > doug > > > > > > > > > On 09/02/2013 12:49 AM, pablo najt wrote: > > > > > > > > Dear FS experts, > > > > I have a doubt about a potential registration problem after running > > > > recon-all -all. I noticed that one of the image outcome when opened > > > > with tkmedit shows no-brain tissue (perhaps eye tracts) ventral to > > > > orbitofrontal areas. I have attached snapshots to illustrate the > > image. > > > > I would greatly appreciate your output on this since I have no > > > > experience with FS and I am not sure what to expect. I would like to > > > > enquire whether I should be concerned about this image or if this is > > > > not a problem. > > > > > > > > Many thanks, > > > > Pablo > > > > > > > > > > > > ___ > > > > 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/ > > ___ > 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] Talairach Failure Detection
Thanks a lot!,Pablo Date: Fri, 30 Aug 2013 11:38:26 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection Hi Pablo yes, any single file that is in the correct series should be fine Bruce On Fri, 30 Aug 2013, pablo najt wrote: > Dear FS, > Following on my question about the initial format of my files for running > recon -all, I finally managed to get the Dicom files for our images. > However, as the imaging protocol includes several modalities, (resting > state, functional, T1, DTI), we had to sort the dicom files. For my > structural data, on which I intend to run FS. Now I get 163 files which I > assume are the number of slices. They look like this: > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627879 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627961 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627880 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627962 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627881 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627963 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627882 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627964 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627883 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627965 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627884 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627966 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627885 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627967 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627886 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627968 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627887 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627969 > > MR.1.3.12.2.1107.5.2.13.20520.300605091339595627888 MR.1.3.12.2.11 > 07.5.2.13.20520.300605091339595627970 > > > > > My question is, for running "recon-all -i john_time1.nii.gz -s > john_time1" which file should I use in the place of "nii.gz" file? Can I use > any of the MR.1.3.12.2 (listed above)? > Many thanks, > Pablo > > > From: pablon...@hotmail.com > To: freesurfer@nmr.mgh.harvard.edu > Date: Tue, 27 Aug 2013 17:14:04 + > Subject: Re: [Freesurfer] Talairach Failure Detection > > Hi I have one last question. I just noticed that my images are in Philips > format. Would you recommend to convert to DICOM anyway? Or should I used > NIFTI?Thanks, > Pablo > > Date: Tue, 27 Aug 2013 12:31:09 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Talairach Failure Detection > > yes, definitely. The dicoms are best > On Tue, 27 Aug 2013, pablo najt wrote: > > > Thank you very much for your input. Yes, I did start with analyze format a > nd also I have visually inspected the images. Almost all my > > scans consistently show an extended whole in the prefrontal area (with a f > ew exception of some scans showing this in posterior > > locations). > > I am assuming the best is to start with either DICOM or NIFTI and avoid an > alyze format. Is this correct? > > > > Best, > > Pablo > > > > > > Date: Tue, 27 Aug 2013 12:08:22 -0400 > > From: fis...@nmr.mgh.harvard.edu > > To: pablon...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Talairach Failure Detection > > > > Hi Pablo > > > > have you visually inspected the talairach xform to see if it is indeed > > incorrect? What input format did you start with? Most of these occur > > because people start with analyze, which doesn't have the direction > > cosines, and so the data is oriented incorrectly > > > > cheers > > Bruce > > > > > > On Tue, 27 Aug 2013, pablo najt wrote: > > > > > Dear FS experts,I am contacting you to report an error after launching r > econ -all for one of my subjects (see below). I am using a > > > macbook pro with snow leopard version 10.6.8. > > > > > > I would greatly appreciate if you could advise me which step/s should I > take to correct this. > > > Thank you for your attention, > > > Pablo > > > > > > Error:-- > --
Re: [Freesurfer] Talairach Failure Detection
Dear FS,Following on my question about the initial format of my files for running recon -all, I finally managed to get the Dicom files for our images. However, as the imaging protocol includes several modalities, (resting state, functional, T1, DTI), we had to sort the dicom files. For my structural data, on which I intend to run FS. Now I get 163 files which I assume are the number of slices. They look like this:MR.1.3.12.2.1107.5.2.13.20520.300605091339595627879 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627961MR.1.3.12.2.1107.5.2.13.20520.300605091339595627880 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627962MR.1.3.12.2.1107.5.2.13.20520.300605091339595627881 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627963MR.1.3.12.2.1107.5.2.13.20520.300605091339595627882 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627964MR.1.3.12.2.1107.5.2.13.20520.300605091339595627883 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627965MR.1.3.12.2.1107.5.2.13.20520.300605091339595627884 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627966MR.1.3.12.2.1107.5.2.13.20520.300605091339595627885 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627967MR.1.3.12.2.1107.5.2.13.20520.300605091339595627886 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627968MR.1.3.12.2.1107.5.2.13.20520.300605091339595627887 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627969MR.1.3.12.2.1107.5.2.13.20520.300605091339595627888 MR.1.3.12.2.1107.5.2.13.20520.300605091339595627970 My question is, for running "recon-all -i john_time1.nii.gz -s john_time1" which file should I use in the place of "nii.gz" file? Can I use any of the MR.1.3.12.2 (listed above)? Many thanks,PabloFrom: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 + Subject: Re: [Freesurfer] Talairach Failure Detection Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote: > Thank you very much for your input. Yes, I did start with analyze format and > also I have visually inspected the images. Almost all my > scans consistently show an extended whole in the prefrontal area (with a few > exception of some scans showing this in posterior > locations). > I am assuming the best is to start with either DICOM or NIFTI and avoid > analyze format. Is this correct? > > Best, > Pablo > > > Date: Tue, 27 Aug 2013 12:08:22 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Talairach Failure Detection > > Hi Pablo > > have you visually inspected the talairach xform to see if it is indeed > incorrect? What input format did you start with? Most of these occur > because people start with analyze, which doesn't have the direction > cosines, and so the data is oriented incorrectly > > cheers > Bruce > > > On Tue, 27 Aug 2013, pablo najt wrote: > > > Dear FS experts,I am contacting you to report an error after launching > > recon -all for one of my subjects (see below). I am using a > > macbook pro with snow leopard version 10.6.8. > > > > I would greatly appreciate if you could advise me which step/s should I > > take to correct this. > > Thank you for your attention, > > Pablo > > > > Error:--- > - > > -- > > #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 > > /Users/pablonajt/subjects/tr5713/mri > > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: > > Tue Jun 7 16:33:36 PDT 2011; > > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > > recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23
Re: [Freesurfer] Talairach Failure Detection
Hi again,I still have a doubt about how to proceed with the processing of my images. Correcting my original response to the format of my images: I ran recon -all -all with NIFTI images (but converted from analyze format). I have converted this by opening them with MRIron and saving as NIFTI.gz (compressed). Should this still produce a talairach failure? If yes, is there any way to convert my analyze images to a compatible format to FS? Sorry that I am going back to the original question, but I just found out from the technicians and our department automatically receives all scans in analyze format. Thank you for your support,Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 + Subject: Re: [Freesurfer] Talairach Failure Detection Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote: > Thank you very much for your input. Yes, I did start with analyze format and > also I have visually inspected the images. Almost all my > scans consistently show an extended whole in the prefrontal area (with a few > exception of some scans showing this in posterior > locations). > I am assuming the best is to start with either DICOM or NIFTI and avoid > analyze format. Is this correct? > > Best, > Pablo > > > Date: Tue, 27 Aug 2013 12:08:22 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Talairach Failure Detection > > Hi Pablo > > have you visually inspected the talairach xform to see if it is indeed > incorrect? What input format did you start with? Most of these occur > because people start with analyze, which doesn't have the direction > cosines, and so the data is oriented incorrectly > > cheers > Bruce > > > On Tue, 27 Aug 2013, pablo najt wrote: > > > Dear FS experts,I am contacting you to report an error after launching > > recon -all for one of my subjects (see below). I am using a > > macbook pro with snow leopard version 10.6.8. > > > > I would greatly appreciate if you could advise me which step/s should I > > take to correct this. > > Thank you for your attention, > > Pablo > > > > Error:--- > - > > -- > > #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 > > /Users/pablonajt/subjects/tr5713/mri > > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: > > Tue Jun 7 16:33:36 PDT 2011; > > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > > recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013 > > > > > > ___ 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 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, p
Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote: > Thank you very much for your input. Yes, I did start with analyze format and > also I have visually inspected the images. Almost all my > scans consistently show an extended whole in the prefrontal area (with a few > exception of some scans showing this in posterior > locations). > I am assuming the best is to start with either DICOM or NIFTI and avoid > analyze format. Is this correct? > > Best, > Pablo > > > Date: Tue, 27 Aug 2013 12:08:22 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Talairach Failure Detection > > Hi Pablo > > have you visually inspected the talairach xform to see if it is indeed > incorrect? What input format did you start with? Most of these occur > because people start with analyze, which doesn't have the direction > cosines, and so the data is oriented incorrectly > > cheers > Bruce > > > On Tue, 27 Aug 2013, pablo najt wrote: > > > Dear FS experts,I am contacting you to report an error after launching > > recon -all for one of my subjects (see below). I am using a > > macbook pro with snow leopard version 10.6.8. > > > > I would greatly appreciate if you could advise me which step/s should I > > take to correct this. > > Thank you for your attention, > > Pablo > > > > Error:--- > - > > -- > > #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 > > /Users/pablonajt/subjects/tr5713/mri > > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: > > Tue Jun 7 16:33:36 PDT 2011; > > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > > recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013 > > > > > > ___ 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 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 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] Talairach Failure Detection
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct? Best,Pablo Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection Hi Pablo have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly cheers Bruce On Tue, 27 Aug 2013, pablo najt wrote: > Dear FS experts,I am contacting you to report an error after launching recon > -all for one of my subjects (see below). I am using a > macbook pro with snow leopard version 10.6.8. > > I would greatly appreciate if you could advise me which step/s should I take > to correct this. > Thank you for your attention, > Pablo > > Error: > -- > #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 > /Users/pablonajt/subjects/tr5713/mri > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) > Manual Talairach alignment may be necessary, or > include the -notal-check flag to skip this test, > making sure the -notal-check flag follows -all > or -autorecon1 in the command string. > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue > Jun 7 16:33:36 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013 > > ___ 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 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] Talairach Failure Detection
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your attention,Pablo Error:--#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013/Users/pablonajt/subjects/tr5713/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)Manual Talairach alignment may be necessary, orinclude the -notal-check flag to skip this test,making sure the -notal-check flag follows -allor -autorecon1 in the command string.See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TalairachDarwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013 ___ 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] Talairach Failure Detection
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects. I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your attention,Pablo Error:--#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013/Users/pablonajt/subjects/tr5713/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)Manual Talairach alignment may be necessary, orinclude the -notal-check flag to skip this test,making sure the -notal-check flag follows -allor -autorecon1 in the command string.See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TalairachDarwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013 ___ 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] Cortical surface
Dear Freesurfer experts, I am interested in running cortical surface area on longitudinal data from MRI scans and run multisubject comparisons (patients vs controls). I would like to ask you where could I find either a tutorial or a guide for performing such analysis. Also I am not familiar with freesurfer, so I am not sure which type of preprocessing should be undertaken.I would greatly appreciate your valuable help on this topic.Pablo ___ 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] Freesurfer installation
Dear Freesurfer experts, I have a question regarding the installation/running of FreeSurfer. I have been trying to install freesurfer in a macbook pro (snow leopard) but no success. I followed the webpage from freesurfer (link below). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup But after the installations when I open the terminal nothing happens. I also tried to launch freesurfer this way: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh If I do this I get: command not found command not found command not found Any advice on how to finally set up the software would be great help. Thank you in anticipation.Pablo ___ 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] environment variable FREESURFER_HOME
Thank you for your answer. There is another issue I am needing help with. As I have edited the .csh file from FreeSurfer I am not able to make it work any more. Is there a way to have a copy of the SetUpFreeSurfer.csh?I have downloaded the last version of Freesurfer for OSX 10.6.8Thank you so much,Pablo > Date: Tue, 11 Jun 2013 11:02:26 -0400 > From: zkauf...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] environment variable FREESURFER_HOME > > Pablo, > > The .cshrc and .bashrc files we are referring to are not Freesurfer files > and do not come with the Freesurfer distribution. They are files that can > (although not always) exist in the home directory of your computer. > > Do not modify the the .csh or .sh files that come with Freesurfer. That is > for the expert user. > > If you want to use Freesurfer just open a command line and type the > following: > > (if using csh) > setenv FREESURFER_HOME Applications/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > (if using bash) > export FREESURFER_HOME=/Applications/freesurfer > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > If you dont want to type these commands everytime you want to start using > freesurfer than you can add these lines to your .csh and .bashrc *in your > home directory*. If those files do not exist than you may create them *in > your home directory* and simply add those two lines to the file. > > -Zeke > > > > > > Dear Freesurfer experts, > > I am trying to install free surfer. > > It seems that my downloaded version does not have a .cshrc file. I only > > have an .sh and .csh file. > > All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source > > Applications/freesurfer/SetUpFreeSurfer.csh) that I tried to the .csh file > > give me "command not found". > > > > Any suggestion would be highly appreciated. > > Pablo > > > > > > > Thank you for your response. > > It seems that my downloaded version does not have a .cshrc file. I only > > have an .sh and a .csh. > > What would you recommend to do? Should I reinstall FreeSurfer? > > Thanks. > > Pablo > > > >> Date: Fri, 7 Jun 2013 18:16:56 -0400 > >> From: zkauf...@nmr.mgh.harvard.edu > >> To: pablon...@hotmail.com > >> Subject: Re: [Freesurfer] environment variable FREESURFER_HOME > >> > >> There should be a file called ".cshrc" in your home directory. Add the > >> two lines to that file. > >> > >> -Zeke > >> > >> On 06/07/2013 05:53 PM, pablo najt wrote: > >> > Can anyone advice me on how to set the environment variable > >> > FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz > >> installed)? > >> > > >> > My directory for Freesurfer:*/Applications/freesurfer* > >> > * > >> > * > >> > I know I also have to add: > >> > > >> > setenv FREESURFER_HOME /Applications/freesurfer > >> > > >> > source $FREESURFER_HOME/SetUpFreeSurfer.csh > >> > But I am not sure where exactly I should add these lines. > >> > > >> > Do I need to edit the .csh file in Freesurfer. > >> > > >> > How should I do this? using Text Edit from apple would work? > >> > Thanks, > >> > Pablo > >> > > >> > > >> > > >> > > >> > ___ > >> > 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 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] Environment variable HOME_FREESURFER
Dear Freesurfer experts, I am trying to install free surfer. It seems that my downloaded version does not have a .cshrc file. I only have an .sh and .csh file. All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source Applications/freesurfer/SetUpFreeSurfer.csh) that I tried to the .csh file give me "command not found". Any suggestion would be highly appreciated. Pablo ___ 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] environment variable FREESURFER_HOME
Can anyone advice me on how to set the environment variable FREESURFER_HOME for installing it in OS X 10.6.8 (with XQuartz installed)? My directory for Freesurfer: /Applications/freesurfer I know I also have to add: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.cshBut I am not sure where exactly I should add these lines. Do I need to edit the .csh file in Freesurfer. How should I do this? using Text Edit from apple would work?Thanks,Pablo ___ 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] Enquire about running FreeSurfer {Disarmed}
As suggested, I have modified the .csh file (since the last version does not
have a .cshrc file).I have edited according with my current directories, but
when I try
source $FREESURFER_HOME/SetUpFreeSurfer.csh
I get the following:
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Setting
up environment for FreeSurfer/FS-FAST (and FSL)WARNING:
/Application/freesurfer//Applications/freesurfer/subjects does not
existFREESURFER_HOME /Applications/freesurfer/FSFAST_HOME
/Applications/freesurfer//fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR
/Application/freesurfer//Applications/freesurfer/subjectsMNI_DIR
/Applications/freesurfer//mni
The editing I made to the .csh file are the following:
setenv FREESURFER_HOME /usr/local/freesurfer/stable5-pub CHANGED TO:setenv
FREESURFER_HOME /Applications/freesurfer/endif
setenv SUBJECTS_DIR $FREESURFER_HOME/subjectsendifCHANGED TO:setenv
SUBJECTS_DIR $FREESURFER_HOME/subjectsendif
Many thanks,Pablo
> Date: Thu, 6 Jun 2013 14:22:07 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
>
>
> You will need to put the FreeSurfer environment variables into your
> .cshrc file to have it be in effect every time you open a new shell.
> doug
>
>
>
>
> On 06/06/2013 02:14 PM, pablo najt wrote:
> > Hello
> > My previous problem seemed to be fixed by reinstalling xquartz.
> > However, the strange thing that I get it that I can perfectly run the
> > following and display the images.
> > This is what I have done. (commands in yellow)
> >
> > * setenv FREESURFER_HOME /Applications/freesurfer/*
> > *source $FREESURFER_HOME/SetUpFreeSurfer.csh*
> >
> > freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME /Applications/freesurfer/
> > FSFAST_HOME /Applications/freesurfer//fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR /Applications/freesurfer/subjects/
> > MNI_DIR /Applications/freesurfer//mni
> > [Pablo-Najts-MacBook-Pro:/Applications/freesurfer] pablonajt%
> >
> > * setenv SUBJECTS_DIR /Applications/freesurfer/subjects/*
> >
> > (After this I am able to run)
> >
> > *freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
> > $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
> > $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
> > $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
> > $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
> > $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red*
> >
> > 2013-06-06 14:07:11.155 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.160 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.183 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.186 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.209 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.212 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.235 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.237 Freeview[624:903] invalid drawable
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> > colortable with 36 entries read (originally
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> > colortable with 36 entries read (originally
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> >
> > *However, eerytime I want to open the display I have to repeat all the
> > commands (setenv FRESURFER... ; source
> > ...; setenv SUBJECTS_DIR)
> >
> > The other problem is that commands such asqdec, tkmedit bert orig.mgz,
> > give
> > "me command not found".
> >
> > Please let me know if I need to provide you with further information.
> > Many thanks,
> > Pablo
> >
> >
> > > Date: Thu, 6 Jun 2013 13:45:42 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: pablon...@hotmail.com; Freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
> > >
> > >
> > > Hi Pablo, please respond to the list and not to us directly.
Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
HelloMy previous problem seemed to be fixed by reinstalling xquartz.However,
the strange thing that I get it that I can perfectly run the following and
display the images.This is what I have done. (commands in yellow)
* setenv FREESURFER_HOME /Applications/freesurfer/* *source
$FREESURFER_HOME/SetUpFreeSurfer.csh*
freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Setting
up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME
/Applications/freesurfer/FSFAST_HOME
/Applications/freesurfer//fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR
/Applications/freesurfer/subjects/MNI_DIR
/Applications/freesurfer//mni[Pablo-Najts-MacBook-Pro:/Applications/freesurfer]
pablonajt%
* setenv SUBJECTS_DIR /Applications/freesurfer/subjects/*
(After this I am able to run)
*freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red*
2013-06-06 14:07:11.155 Freeview[624:903] invalid drawable2013-06-06
14:07:11.160 Freeview[624:903] invalid drawable2013-06-06 14:07:11.183
Freeview[624:903] invalid drawable2013-06-06 14:07:11.186 Freeview[624:903]
invalid drawable2013-06-06 14:07:11.209 Freeview[624:903] invalid
drawable2013-06-06 14:07:11.212 Freeview[624:903] invalid drawable2013-06-06
14:07:11.235 Freeview[624:903] invalid drawable2013-06-06 14:07:11.237
Freeview[624:903] invalid drawablereading colortable from annotation
file...colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)colortable
with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)reading
colortable from annotation file...colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)colortable
with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
*However, eerytime I want to open the display I have to repeat all the commands
(setenv FRESURFER... ; source...; setenv SUBJECTS_DIR)
The other problem is that commands such as qdec, tkmedit bert orig.mgz, give
"me command not found".
Please let me know if I need to provide you with further information.Many
thanks,Pablo
> Date: Thu, 6 Jun 2013 13:45:42 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: pablon...@hotmail.com; Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
>
>
> Hi Pablo, please respond to the list and not to us directly. Please just
> cut and paste the text of the error into the email.
> thanks
> doug
>
> On 06/06/2013 12:30 PM, pablo najt wrote:
> > Thank you for your quick response. I have re run the installation but
> > I get the following erros with _tkmedit bert orig.mgz_ and _tksurfer
> > bert rh pial_ commands.
> > Please see attach for the detailed errors.
> > Best,
> > Pablo
> >
> >
> > > Date: Thu, 6 Jun 2013 12:01:22 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
> > >
> > > what command is not found?
> > > On 06/06/2013 11:58 AM, pablo najt wrote:
> > > > Hello I have a question regarding the installation/running FreeSurfer.
> > > > I have just completed the installation and got the confirmation that
> > > > Free surfer was installed. Please see snapshot.
> > > > However when I follow the steps for testing (*MailScanner has
> > detected
> > > > a possible fraud attempt from "connect.yale.edu" claiming to be*
> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
> > > >
> > <https://connect.yale.edu/owa/14.3.123.3/scripts/premium/redir.aspx?C=Alh1YjfYCUe8ElP16xL_q_5yptViNtAIG4dh8kuWzHm46SgPyyH76vPaU4_Khh3GCekIs1EN4G4.&URL=https%3a%2f%2fsurfer.nmr.mgh.harvard.edu%2ffswiki%2fTestingFreeSurfer>),
> >
> >
> > > > I always get "command not found". I was wondering if you would be
> > able
> > > > to help me.
> > > > Thanks,
> > > > Pablo
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees
[Freesurfer] Enquire about running FreeSurfer {Disarmed}
Hello I have a question regarding the installation/running FreeSurfer.I have just completed the installation and got the confirmation that Free surfer was installed. Please see snapshot.However when I follow the steps for testing (https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer), I always get "command not found". I was wondering if you would be able to help me.Thanks,Pablo <>___ 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.
