Re: [Freesurfer] How to get surface-based AAL template

[Garikoitz Lerma-Usabiaga]

Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest version.
Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't know
the exact differences between fs mni305 and fs mnicolin27. What I know is
that going the fsaverage path I couldn't obtain reliable transformations of
the AAL labels. I think this was because fsaverage is very smoothed.
Spm_register and vol2surf weren't working well.

The thing is, for group analysis, you can use Colin (or any other), as I
understood it. When you use -qcache your data goes to fsaverage, but you
can do it manually and specify that you want Colin instead (maybe someone
can confirm it). If you are going to use just the AAL average CTs, then you
just need to use surf2surf or label2label and you won't need fsaverage at
all.

3- well, the spm single subject and Colin from Surfrend are the same
subject but not exactly the same image. You do bbregister to them and
obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm
and has some minimal translation. If you see both T1-s with tkregister you
will see that they are almost the same (the spm version a little bit
blurred, because of the resolution). You use this register.dat when doing
vol2surf of the AAL.nii to your AAL.mgh surface ROI.

Hope this helps!
Gari

On 27/03/2013, at 14:06, ZhiLiangLong  wrote:

Dear Br:
   Thanks for your help. I have downloaded Colin 27 subject, and the
Surfrend toolbox. But I still have some questions about the process.
   1. You said I need transform the Colin 27 to the latest FS version
(v.5.2). But i don't know how to do this. It is helpful if you can provide
some information.

  2. How does the Colin 27 space differs from fsaverage MNI305 space? The
group analysis of cortical thickness is conducted in fsaverage space, after
importing AAL ROI into Colin 27 space, should i  transform the obtained ROI
into fsaverage space?
 3. i don't understand what is the register.dat between COlin 27 and SPM-s
single subject t1.nii used for? I have tried the Surfrend, and found there
was no entry for input of register file during the processing.

Looking forward to your reply.
Best wishes.

zhiliang



At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" 
wrote:

Hi,
In my case transformation to fsaverage did not work very well. What I did
was:
-  from Surfrend page download Colin 27 subject and transform it to the
latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and
SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s
are defined in Colin 27. As they are the same subject, the registering is
very good.
- now you can import every AAL ROI (in .nii form) to an annotation or in
the form of individual labels to your FS Colin 27, using the newly created
registering file.
- now you can use surf2surf or label2label to go to your subjects and
obtain stats.

Br!

On 27/03/2013, at 05:35, ZhiLiangLong  wrote:

Hi all;
  I need a suface-based aal template which is compatible with FS
surface file. Is there a way i can get the surface-based aal template? I
have an idea, that is to just transform the AAL template (.nii file) in MNI
space onto the surface template (e.g. fsaverage template) in FS. Is it
correct? if in this case, how can i do the transformation?

Any suggestions appreciated.
Besh wishes.


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[Freesurfer] Download problem wih freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg

[Leila Reddy]

Hi,

I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I 
click on the download link I get an error: 550 Failed to change directory.
I can't find a file with this filename in 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ either. Is this version 
not yet available (and when will it be available)?

Thanks,
Leila
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Re: [Freesurfer] Download problem wih freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg

[Bruce Fischl]

Hi Leila

we found a problem with the mac build that we are fixing. We will put it 
up again soon, hopefully today.

sorry
Bruce
On Fri, 29 Mar 2013, Leila Reddy wrote:

> Hi,
>
> I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I
> click on the download link I get an error: 550 Failed to change directory.
> I can't find a file with this filename in
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ either. Is this version
> not yet available (and when will it be available)?
>
> Thanks,
> Leila
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] trac-all -path error

[Anastasia Yendiki]

Hi Nawaf - The first error occured much earlier in the log file. Your 
gradient table file could not be found. Did you set the bvecfile variable 
in your configuration file?


a.y

On Fri, 29 Mar 2013, Nawaf Yassi wrote:


Hi Anastasia
Thanks for your reply
Here is the file attached (I have replaced the subject's name with 'A'
for anonymity)
Regards
Nawaf


On 29/03/13 2:17 AM, "Anastasia Yendiki" 
wrote:




Hi Nawaf - Can you please send your trac-all.log? It's possible that the



problem started at an earlier step.

Thanks,
a.y

On Thu, 28 Mar 2013, Nawaf

Yassi wrote:



Dear mailing list

I am encountering an error at the
trac-all ­path stage of a tracula analysis (the
first two stages on trac-all
seem to have run ok) with the appropriate outputs. I am
getting the error
³Segmentation fault² (core dumped) very early on after the
dmri_paths
command is run (see below). Can anyone help?

I am using freesurfer 5.2
and FSL 5.0.2.1 (linux)
Regards
Nawaf
ATTACHED: ERROR MESSAGE + config
file below

=


[nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject
Too many
)'s.
INFO: SUBJECTS_DIR is

/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer

INFO: Diffusion root is

/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer

Actual FREESURFER_HOME /usr/local/freesurfer5.2
trac-paths
-c/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01
/scripts/
dmrirc.local
-log/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C
01/scripts/
trac-all.log
-cmd/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C
01/scripts/
trac-all.cmd
#-

/usr/local/freesurfer5.2/bin/trac-paths

#-
#@# Path reconstruction Thu Mar 28
10:01:34 EST 2013
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.cst_AS_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.cst_AS_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.ilf_AS_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.ilf_AS_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.unc_AS_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.unc_AS_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/fm
ajor_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/fm
inor_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.atr_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.atr_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.ccg_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.ccg_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.cab_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.cab_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.slfp_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.slfp_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/lh
.slft_PP_avg33_mni_bbr
rm
-rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0
1/dpath/rh
.slft_PP_avg33_mni_bbr
/usr/local/freesurfer5.2/bin/dmri_paths
--outdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf
er/C01/dpath/lh

.cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/rh

.cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/lh

.ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/rh

.ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/lh

.unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/rh

.unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/fm

ajor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/fm

inor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis
/C01_freesurfer/C01/dpath/lh

.atr_PP_avg33_mni_bbr/bi

[Freesurfer] Problem with longitudinal edits

[Vy Dinh]

Dear Developers,

I have a significant problem when rerunning the pial edits for the
longitudinal data. Our dataset consists of subjects & a followup scan (for
each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it
was further in the processing stream) for the cross-sectional scans, the
base scans, and the longitudinal scans. The longitudinal data were created
only after the base has been edited and rerun. Likewise, the base was only
created and rerun after the cross-sectionals were finalized.

We work with a clinical population so minor edits do show up on the
longitudinal scans. However, after editing and recreating the surfaces from
these longitudinal scans, the pial surfaces has extended to include dura &
other voxels that were not previously included within the pial surface
(during the initial creation of the longitudinal data). We tried both
commands (listed below) and get this same problem:

recon-all -autorecon2-pial -autorecon3 -long tpN tp_base (
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits)
or recon-all -autorecon3-pial -long tpN tp_base  (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)

*Could you please help us figure out why the pial surface extends to
include nonbrain regions when recreating the surfaces? *
*
*
*What solutions would you suggest in resolving this problem?*
*
*
Thank you,

Vy Dinh
Research Associate
Department of Neurological Sciences
Rush University Medical Center
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Re: [Freesurfer] Problem with longitudinal edits

[Vy Dinh]

BTW, we are using Freesurfer 5.1:
freesurfer-i686-apple-darwin9.8.0-stable5-20110525


On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh  wrote:

> Dear Developers,
>
> I have a significant problem when rerunning the pial edits for the
> longitudinal data. Our dataset consists of subjects & a followup scan (for
> each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it
> was further in the processing stream) for the cross-sectional scans, the
> base scans, and the longitudinal scans. The longitudinal data were created
> only after the base has been edited and rerun. Likewise, the base was only
> created and rerun after the cross-sectionals were finalized.
>
> We work with a clinical population so minor edits do show up on the
> longitudinal scans. However, after editing and recreating the surfaces from
> these longitudinal scans, the pial surfaces has extended to include dura &
> other voxels that were not previously included within the pial surface
> (during the initial creation of the longitudinal data). We tried both
> commands (listed below) and get this same problem:
>
> recon-all -autorecon2-pial -autorecon3 -long tpN tp_base (
> http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits)
> or recon-all -autorecon3-pial -long tpN tp_base  (
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
>
> *Could you please help us figure out why the pial surface extends to
> include nonbrain regions when recreating the surfaces? *
> *
> *
> *What solutions would you suggest in resolving this problem?*
> *
> *
> Thank you,
>
> Vy Dinh
> Research Associate
> Department of Neurological Sciences
> Rush University Medical Center
>
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Re: [Freesurfer] bbr problem run

[Anastasia Yendiki]

Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out 
if it's 5.2-specific.


Thanks,
a.y

On Thu, 28 Mar 2013, Salil Soman wrote:


Thank you for your response. 
I tried re-running Tracula using bbr in a subject I had successfully run using 
flt.
trac-all prep and bedp worked without an error. Bedpostx sent me an email 
confirming
bedpost completed without problem. However, when I try to run trac-all paths, I 
get
the following error:

Loading atlas reference volume 
from/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end
1_dil.nii.$
niiRead(): error opening 
file/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end
1_dil.nii.gz
ERROR: Could not 
read/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end
1_dil.nii.gz

recon-all did finish without error.

Best wishes,

-S


On Thu, Mar 28, 2013 at 8:43 AM, Anastasia
Yendiki  wrote:

  Hi Sal,

  1. I have no experience with the sun grid engine, perhaps someone else on
     the list can help with that.

  2. The -bedp step needs the outputs from the -corr and -masks steps. The
     -path step needs the outputs from the -bedp step. The output files from
     each part are listed here:
     http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles

  3. Checking the aparc+aseg should be enough for tracula purposes as well,
     since that's the freesurfer output that tracula uses. Keep in mind that
     DWI resolution is usually lower than T1 resolution, so tiny changes in
     the aparc+aseg might not affect tracula at all.

  4. Yes, I do recommend using bbregister. It's not surprising that it would
     give better results since it uses the additional information of the
     surfaces. If I remember correctly, Doug didn't manage to replicate your
     bbregister error, right? I'd check if you get the same error with the
     5.1 version of bbregister.

  Hope this helps,
  a.y

  On Wed, 27 Mar 2013, Salil Soman wrote:

Hi,
I have been able to implement FS 5.2 on our Sun Grid Engine
Cluster using the CentOS 6
distribution. After modifying the fsl_sub_mgh file to work
with out cluster queue
names and to modify the email notifications, I am able to run
the entire processing
pipeline using FLT. (Everytime I try bbr I get errors. I had
email doug about this but
have not heard any response).

I am submitting the jobs to the cluster as follows

recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T
-nocanorm -openmp 50
-hippo-subfields -all
trac-all -prep -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
trac-all -bedp -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
trac-all -path -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc 

There are a few issues I am trying to sort out:

1) how should one conifigure the openmp flag for the Sun Grid
Engine? the flag I used
did not change processing time, and each subject is still
taking ~24 hrs?

2) once the script starts bedpost, bedpost has controller code
which paralelizes all
of the slices (which has been great going from 12 hrs of
processing to 1.5 hrs).
However, my original script goes on to execute trace-all -path
... before bepost is
done, generating errors. I have gotten around this by running
the trace-all -path
command again after bedpost sends me an email confirming
completion. Is there a way to
more cleanly do this (some kind of hold command I can do based
on output from
bedpost)?

3) In your experience, how important is quality control of
freesurfer on tracula
results? We have come to the compromise for freesurfer output
to manually check the
segmentation of aparc+aseg.mgz using free view, only
correcting and rerunning steps of
freesurfer when there are specific structures we want the
volumes of (eg hippocampus).

4) have you found a significant benefit of bbr over flt? If
so, any suggestions on
things I may need to check to get bbr to work (given flt
works)?

Best wishes,

Sal








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[Freesurfer] slice timing

[Meryem Ayse Yucel]

Hi,

I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am
wondering when I do slice time correction does that move all slices to the
mid of TR that is 1.5 s prior in time or, it moves them to the timing of
the mid slice, which would be the mid of image acquisition aorund 0.6 sec
prior in time with respect to the end of TR.

Thank you,

Meryem
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Re: [Freesurfer] bbr problem run

[Anastasia Yendiki]

Hi Sal - Would it be possible for you to run the bbregister command that 
fails (you can find the command line in trac-all.log) using both the 5.1 
and 5.2 version of bbregister and see if one of them works on your system?


a.y

On Fri, 29 Mar 2013, Salil Soman wrote:


Hi Anastasia,

Because I did not have a compatible older version of fsl on the SGE, I was not 
able to
run tracula with 5.1.

Thank you,

Sal


On Fri, Mar 29, 2013 at 8:32 AM, Anastasia Yendiki 

wrote:

  Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out
  if it's 5.2-specific.

  Thanks,
  a.y

  On Thu, 28 Mar 2013, Salil Soman wrote:

Thank you for your response. 
I tried re-running Tracula using bbr in a subject I had
successfully run using flt.
trac-all prep and bedp worked without an error. Bedpostx sent
me an email confirming
bedpost completed without problem. However, when I try to run
trac-all paths, I get
the following error:

Loading atlas reference 
volumefrom/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr
_end
1_dil.nii.$
niiRead(): error 
openingfile/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr
_end
1_dil.nii.gz
ERROR: Could 
notread/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr
_end
1_dil.nii.gz

recon-all did finish without error.

Best wishes,

-S


On Thu, Mar 28, 2013 at 8:43 AM, Anastasia
Yendiki  wrote:

      Hi Sal,

      1. I have no experience with the sun grid engine,
perhaps someone else on
         the list can help with that.

      2. The -bedp step needs the outputs from the -corr and
-masks steps. The
         -path step needs the outputs from the -bedp step. The
output files from
         each part are listed here:
       
 http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles

      3. Checking the aparc+aseg should be enough for tracula
purposes as well,
         since that's the freesurfer output that tracula uses.
Keep in mind that
         DWI resolution is usually lower than T1 resolution,
so tiny changes in
         the aparc+aseg might not affect tracula at all.

      4. Yes, I do recommend using bbregister. It's not
surprising that it would
         give better results since it uses the additional
information of the
         surfaces. If I remember correctly, Doug didn't manage
to replicate your
         bbregister error, right? I'd check if you get the
same error with the
         5.1 version of bbregister.

      Hope this helps,
      a.y

      On Wed, 27 Mar 2013, Salil Soman wrote:

            Hi,
            I have been able to implement FS 5.2 on our Sun
Grid Engine
            Cluster using the CentOS 6
            distribution. After modifying the fsl_sub_mgh file
to work
            with out cluster queue
            names and to modify the email notifications, I am
able to run
            the entire processing
            pipeline using FLT. (Everytime I try bbr I get
errors. I had
            email doug about this but
            have not heard any response).

            I am submitting the jobs to the cluster as follows

            recon-all -i ./*.nii -s WCA_0202_T1_FS
-nuintensitycor-3T
            -nocanorm -openmp 50
            -hippo-subfields -all
            trac-all -prep -no-isrunning -c
            /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
            trac-all -bedp -no-isrunning -c
            /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
            trac-all -path -no-isrunning -c
           
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc 

            There are a few issues I am trying to sort out:

            1) how should one conifigure the openmp flag for
the Sun Grid
            Engine? the flag I used
            did not change processing time, and each subject
is still
            taking ~24 hrs?

            2) once the script starts bedpost, bedpost has
 

[Freesurfer] mris_preproc with --xhemi

[Ejoe Yizhou Ma]

Hi freesurfer experts,

I'm investigating lh-to-rh asymmetry and am following instructions on this
page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi.
My question is, what does the "--xhemi" flag do in the "mris_preproc"
command? It seems to me that it calculates (lh-rh) value at each vertex for
every subject. (I tried to use the same subject for each pair of input for
"--paired-diff", and the result is not a all-zero output.)

It would also be nice if someone can tell me how to realize my final goal,
which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each
subject in a .mgh file.

Thanks,
Cherry
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Re: [Freesurfer] mris_preproc with --xhemi

[Douglas N Greve]

The --xhemi flag causes both the left and right hemispheres of each 
subject to be stacked into the output file. So the output file will have 
number of subjects x2 frames. The order is subject1.lh, subject1.rh, 
subject2.lh, subject2.rh, ...

If you add the --paired-diff, then you will get number of frames = 
number of subjects, and each frame will be subject1.lh-rh, 
subject2.lh-rh, etc

If you use the --paired-diff-norm instead, then you will get what you 
want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc.

Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would 
need to multiply the paired-diff-norm by 2.

Finally, I want to point out that it may be better to smooth before 
computing the LI because the LI computation is non-linear and it has the 
potential to divide by a noisy number. To do this, run without the 
--paired-diff flags, then smooth, then run

mri_concat yourfile.smoothed.mgh --paired-diff-norm --o 
yourfile.smoothed.LI.mgh

In my study, I ran it both ways and it did not make a difference, but I 
think smoothing before LI is the safer bet.

doug


On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote:
> Hi freesurfer experts,
>
> I'm investigating lh-to-rh asymmetry and am following instructions on 
> this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi.
> My question is, what does the "--xhemi" flag do in the "mris_preproc" 
> command? It seems to me that it calculates (lh-rh) value at each 
> vertex for every subject. (I tried to use the same subject for each 
> pair of input for "--paired-diff", and the result is not a all-zero 
> output.)
>
> It would also be nice if someone can tell me how to realize my final 
> goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for 
> each subject in a .mgh file.
>
> Thanks,
> Cherry
>
>
> ___
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mris_preproc with --xhemi

[Ejoe Yizhou Ma]

Thanks, Doug. This is very helpful!


On Fri, Mar 29, 2013 at 12:48 PM, Douglas N Greve  wrote:

> The --xhemi flag causes both the left and right hemispheres of each
> subject to be stacked into the output file. So the output file will have
> number of subjects x2 frames. The order is subject1.lh, subject1.rh,
> subject2.lh, subject2.rh, ...
>
> If you add the --paired-diff, then you will get number of frames =
> number of subjects, and each frame will be subject1.lh-rh,
> subject2.lh-rh, etc
>
> If you use the --paired-diff-norm instead, then you will get what you
> want subject1.(lh-rh)/((lh+rh)/2), subject2.(lh-rh)/((lh+rh)/2), etc.
>
> Note that most laterality indices (LI) are (lh-rh)/(lh+rh), so you would
> need to multiply the paired-diff-norm by 2.
>
> Finally, I want to point out that it may be better to smooth before
> computing the LI because the LI computation is non-linear and it has the
> potential to divide by a noisy number. To do this, run without the
> --paired-diff flags, then smooth, then run
>
> mri_concat yourfile.smoothed.mgh --paired-diff-norm --o
> yourfile.smoothed.LI.mgh
>
> In my study, I ran it both ways and it did not make a difference, but I
> think smoothing before LI is the safer bet.
>
> doug
>
>
> On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote:
> > Hi freesurfer experts,
> >
> > I'm investigating lh-to-rh asymmetry and am following instructions on
> > this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi.
> > My question is, what does the "--xhemi" flag do in the "mris_preproc"
> > command? It seems to me that it calculates (lh-rh) value at each
> > vertex for every subject. (I tried to use the same subject for each
> > pair of input for "--paired-diff", and the result is not a all-zero
> > output.)
> >
> > It would also be nice if someone can tell me how to realize my final
> > goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for
> > each subject in a .mgh file.
> >
> > Thanks,
> > Cherry
> >
> >
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] slice timing

[Douglas N Greve]

what are you using to do STC? I think by default FSL will move it to the 
middle slice, but there is probably a way to make take into account the 
fact that the slices are not uniform over the TR. You should contact the 
list of the software you are using to get a definative answer.
doug


On 03/29/2013 11:37 AM, Meryem Ayse Yucel wrote:
> Hi,
>
> I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am
> wondering when I do slice time correction does that move all slices to the
> mid of TR that is 1.5 s prior in time or, it moves them to the timing of
> the mid slice, which would be the mid of image acquisition aorund 0.6 sec
> prior in time with respect to the end of TR.
>
> Thank you,
>
> Meryem
> ___
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> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] selxavg3-sess problem with -per-run flag

[SHAHIN NASR]

Hi,
 I used to run my mkanalysis-sess without indicating -per-run or
-per-session, assuming that when I have pre-processed my files with
-per-run flag then selxavg3-sess will do the same. But when I checked the
analysis.info I noticed  "PerSession 1" which I think it means system will
use per-session preprocessing. So, this time I explicitly used -per-run in
my mkanalysis-sess as below:

preproc-sess -s  -per-run -fwhm 5 -fsd bold -fwhm 5 -surf self rhlh

mkanalysis-sess -analysis Reward.rh -surface self rh -native -fwhm 5
-paradigm Conds.par -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg
-TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run -force

This time when I ran selxavg3-sess command I faced this error:

ERROR: cannot determine format of
/autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5
(MRIread)


Error in flac_customize (line 87)
mri = MRIread(fstem,1);

Error in fast_selxavg3 (line 65)
flac0 = flac_customize(flac0);

>> --
ERROR: fast_selxavg3() failed\n


As I checked my subjects directory I had these files in /bold/004/
directory:

fmcpr.nii.gz
fmcpr.sm5.self.rh.nii.gz
fmcpr.sm5.self.lh.nii.gz

Notably, if I drop that -per-run flag from my mkanalysis-sess then system
works without any problem. But then I am not sure whether I have processed
my data in per-run or per-session mode.

Any help will be appreciated
Regards


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] bbr problem run

[Douglas N Greve]

There was a problem with bbregister running on the new CentOS 6 
machines. I've attached a new version that should work.

doug


On 03/29/2013 11:41 AM, Anastasia Yendiki wrote:


Hi Sal - Would it be possible for you to run the bbregister command 
that fails (you can find the command line in trac-all.log) using both 
the 5.1 and 5.2 version of bbregister and see if one of them works on 
your system?


a.y

On Fri, 29 Mar 2013, Salil Soman wrote:


Hi Anastasia,

Because I did not have a compatible older version of fsl on the SGE, 
I was not able to

run tracula with 5.1.

Thank you,

Sal


On Fri, Mar 29, 2013 at 8:32 AM, Anastasia Yendiki 


wrote:

  Hi Sal - Had you ever tried running this in 5.1? Just trying to 
figure out

  if it's 5.2-specific.

  Thanks,
  a.y

  On Thu, 28 Mar 2013, Salil Soman wrote:

Thank you for your response.
I tried re-running Tracula using bbr in a subject I had
successfully run using flt.
trac-all prep and bedp worked without an error. Bedpostx 
sent

me an email confirming
bedpost completed without problem. However, when I try to 
run

trac-all paths, I get
the following error:

Loading atlas reference 
volumefrom/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr

_end
1_dil.nii.$
niiRead(): error 
openingfile/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr

_end
1_dil.nii.gz
ERROR: Could 
notread/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr

_end
1_dil.nii.gz

recon-all did finish without error.

Best wishes,

-S


On Thu, Mar 28, 2013 at 8:43 AM, Anastasia
Yendiki  wrote:

  Hi Sal,

  1. I have no experience with the sun grid engine,
perhaps someone else on
 the list can help with that.

  2. The -bedp step needs the outputs from the -corr and
-masks steps. The
 -path step needs the outputs from the -bedp 
step. The

output files from
 each part are listed here:

 http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles

  3. Checking the aparc+aseg should be enough for 
tracula

purposes as well,
 since that's the freesurfer output that tracula 
uses.

Keep in mind that
 DWI resolution is usually lower than T1 resolution,
so tiny changes in
 the aparc+aseg might not affect tracula at all.

  4. Yes, I do recommend using bbregister. It's not
surprising that it would
 give better results since it uses the additional
information of the
 surfaces. If I remember correctly, Doug didn't 
manage

to replicate your
 bbregister error, right? I'd check if you get the
same error with the
 5.1 version of bbregister.

  Hope this helps,
  a.y

  On Wed, 27 Mar 2013, Salil Soman wrote:

Hi,
I have been able to implement FS 5.2 on our Sun
Grid Engine
Cluster using the CentOS 6
distribution. After modifying the fsl_sub_mgh 
file

to work
with out cluster queue
names and to modify the email notifications, 
I am

able to run
the entire processing
pipeline using FLT. (Everytime I try bbr I get
errors. I had
email doug about this but
have not heard any response).

I am submitting the jobs to the cluster as 
follows


recon-all -i ./*.nii -s WCA_0202_T1_FS
-nuintensitycor-3T
-nocanorm -openmp 50
-hippo-subfields -all
trac-all -prep -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
trac-all -bedp -no-isrunning -c
/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc
trac-all -path -no-isrunning -c

/mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc

There are a few issues I am trying to sort out:

1) how should one conifigure the openmp flag for
the Sun Grid
Engine? the flag I used
did not change processing time, and each subject
is still
   

Re: [Freesurfer] selxavg3-sess problem with -per-run flag

[Douglas N Greve]

You have specified both -surface and -native which conflict with each 
other. In this case, it will use native space which forces it to use 
per-session (no way to avoid  this).
doug


On 03/29/2013 01:08 PM, SHAHIN NASR wrote:
> Hi,
>  I used to run my mkanalysis-sess without indicating -per-run or 
> -per-session, assuming that when I have pre-processed my files with 
> -per-run flag then selxavg3-sess will do the same. But when I checked 
> the analysis.info  I noticed  "PerSession 1" 
> which I think it means system will use per-session preprocessing. So, 
> this time I explicitly used -per-run in my mkanalysis-sess as below:
>
> preproc-sess -s  -per-run -fwhm 5 -fsd bold -fwhm 5 -surf self 
> rhlh
>
> mkanalysis-sess -analysis Reward.rh -surface self rh -native -fwhm 5 
> -paradigm Conds.par -event-related -polyfit 2 -gammafit 2.25 1.25 
> -mcextreg -TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run 
> -force
>
> This time when I ran selxavg3-sess command I faced this error:
>
> ERROR: cannot determine format of
> /autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5
> (MRIread)
>
>
> Error in flac_customize (line 87)
> mri = MRIread(fstem,1);
>
> Error in fast_selxavg3 (line 65)
> flac0 = flac_customize(flac0);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
>
> As I checked my subjects directory I had these files in /bold/004/ 
> directory:
>
> fmcpr.nii.gz
> fmcpr.sm5.self.rh.nii.gz
> fmcpr.sm5.self.lh.nii.gz
>
> Notably, if I drop that -per-run flag from my mkanalysis-sess then 
> system works without any problem. But then I am not sure whether I 
> have processed my data in per-run or per-session mode.
>
> Any help will be appreciated
> Regards
>
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] FS version of Colin27

[Douglas N Greve]

If you have the T1 for colin27, then just run recon-all on it.
doug


On 03/29/2013 01:48 AM, ZhiLiangLong wrote:
> Hi FS experts:
> I am trying to map AAL template onto FS surface to create 
> surface-based AAL template. Several days ago, i asked this question, 
> and Garikoitz Lerma gave me some suggestions. Possibly, i think the 
> process is like as folllows:
>1.  downloa the Colin27 subject in Surfrend page, and transform it 
> to the latest FS version (5.2 currently).
>2. obtain register.dat between Colin27 subject and 
> single_subj_T1.nii under the /canonical/ directory in SPM8 using 
> bbregister.
> bbregister --s Colin27_subject  --mov single_subj_T1.nii  --reg 
> register.dat  --init-fsl  --t1
> 3. transfrom each AAL ROI to the surface file with register.dat file 
> obtained above using mri_vol2surf.
>mri_vol2surf --mov AAL_ROI.nii  --reg register.dat  --projdist-max 
> 0 1 0.1  --interp nearest  --hemi lh \
>   --out lh.Colin27_AALROI.mgh  --reshape
> 4. use mri_label2label or mri_segstat to obtain the cortical thickness 
> of each ROI for individual subject.
> My question is about the first step.  How to transform the Colin27 
> subject to FS version 5.2? that is to say  how can i get the FS 
> version of Colin27 template instead of fsaverage template?
> Hope so meone gives me some suggetions.
> Besh wishes.
>
>
>
>
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Re: [Freesurfer] Error from mri_concat while using QDEC

[Douglas N Greve]

If yyou just type mri_concat at the command line and nothting happens, 
then something is definitely wrong. What system are you running on?


On 03/28/2013 04:17 PM, Tudor Popescu wrote:
> I tried running it by itself, to remind me of the syntax, so that I 
> can do a simple concatenation to see if it works. But after typing 
> mri_concat and hitting Enter, nothing happens, I'm just returned to 
> the command prompt.
>
> The same happens if I type the following command, from the folder 
> containing the two input files
> mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz
>
> Could this indicate something is wrong with the mri_concat command itself?
>
> On 28 March 2013 20:01, Douglas N Greve  > wrote:
>
>
> Sorry, I've totally lost track of this thread. Are you able to run
> mri_concat outside of QDEC?
>
>
> On 03/28/2013 03:51 PM, Tudor Popescu wrote:
> > Still stuck with this error in my QDEC analysis attempt, at my wit's
> > end, could anyone help please? Thanks!
> > Tudor
> >
> > On 26 March 2013 20:35, Tudor Popescu  
> > >> wrote:
> >
> > Just giving this thread a new bump, as /again /I am
> receiving this
> > error from mri_concat, upon pressing the Analyze button in QDEC.
> > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly
> (and
> > includes a copy of the fsaverage folder) and all files
> included in
> > the error are at the expected path. Screenshot attached.
> >
> >
> > On 18 March 2013 11:20, Tudor Popescu  
> > >> wrote:
> >
> > Hi Andreas
> >
> > I don't think it's about the OS (I'm on WInXP SP3, 32 bit,
> > hosting Linux using Vritualbox), but about the environment
> > variables, even though from what I could see, I had them all
> > correctly set. I gave up and am just running this
> through FSL..
> >
> > Tudor
> >
> >
> > On 18 March 2013 11:13, Andreas Berger
> >  
> >  >> wrote:
> >
> > On Friday, February 01, 2013 17:12:00 Tudor Popescu
> wrote:
> > > Hi Doug
> > >
> > > Strangely, the basic mri_concat command now
> worked, and
> > so did the full
> > > one. I think I initially had a "\" at the end of my
> > command, just after the
> > > file name, which should not have been there; although
> > having tried again
> > > with the backslash reinstated at the end, the command
> > still worked. Also,
> > > the Analyze in the QDEC GUI now completes without
> error
> > as well.
> > >
> > > It's quite frustrating that I still don't know why it
> > hasn't been working
> > > all this time, especially since I didn't really do
> > anything different now
> > > (that I was aware of!) and the files were located
> on the
> > same partition
> > > (Virtualbox's shared folder).
> > >
> > > Anyhow, thanks again for your kind help!
> > >
> > > Tudor
> > >
> > > On 31 January 2013 20:36, Douglas N Greve
> >  
> >  >> wrote:
> > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote:
> > > >> Hi Doug,
> > > >>
> > > >> I'm not sure why that does not make sense,
> shouldn't
> > the input of
> > > >> mri_concat be several to-be-concatenated files
> rather
> > than a single
> > > >> file?
> > > >
> > > > Sorry, I did not mean to imply that the command line
> > was wrong, rather
> > > > that the behavior did not make sense -- it should
> > print *something* to
> > > > the terminal. It does make sense to have multiple
> > files, but it will
> > > > also work with a single file. I just suggested
> this to
> > make things
> > > > simpler.
> > > >
> > > >> Anyway, after trying out the command with only
> one of
> >   

Re: [Freesurfer] Use a SPM roi to extract thickness measurements

[Douglas N Greve]

Hi Stephanie, in your mri_vol2surf cmd, try using --projfrac-max -.2 1.2 .1
This will search for the max along the vector normal to the surface 20% 
below the white matter and 20% beyond the pial.
doug


On 03/27/2013 04:42 PM, McMains, Stephanie wrote:
> Hi all,
>
> I have been trying to take an SPM volume and extract FS thickness 
> measurements.
>
> I think I successfully took my spm volume from mni152 to fsaverage space 
> (mni305) via the command line:
>
> mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/mni305.cor.mgz 
> --targ RTPJ_9mm_001_10_64_-54_16.img --reg 
> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --inv --o  
> $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz
>
> Then I turned it into an ROI:
>
> mri_binarize --i 
> $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz --o 
> $SUBJECTS_DIR/2506/mri/RTPJ_mni305_roi_9mm_001_10_64_-54_16.nii.gz --min 
> .01
>
>>  From here I figured I could map it to the fsaverage surface (mri_vol2surf) 
>> and extract thickness measurements (mri_segstats using 
>> rh.thickness.fsaverage.mgh) as suggested in the volume roi cortical 
>> thickness workflow. However, some of my ROIs don't show up after I transform 
>> them.  From what I can tell, this is because they don't intersect with the 
>> fsaverage surface.
> My thinking was that it might be better to stay within the individual subject 
> space.  So I would:
>
> 1. transform ROI to subject space
> 2. extract thickness values from rh.thickness
>
> However, I am struggling to get the roi into single subject space.  I feel 
> like this transform (or the inverse of it) should exist because I put all my 
> subjects into fsaverage space via the -qcache flag, but i couldn't tell what 
> to use.
>
> So I tried:
>
> fslregister --s 2506 --mov $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg 
> $SUBJECTS_DIR/2506/fsaverage_to_indiv.dat
>
> But the registration doesn't look all that good.  I am not sure if this is 
> because the fsaverage is 'smoothed' or what.
>
> And then I am at a loss for how to put my roi into individual space and then 
> extract thickness, or even if this is the right approach.
>
> Thanks,
> Stephanie
>
>
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>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] slice timing

[MCLAREN, Donald]

If you are using ASL, you do not want to use Slice timing. You must compute
the CBF maps and keep the slice timing intact.

Removing the time delay between slices will lead to the wrong CBF values as
the CBF equations have the time delay in the equation.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
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On Fri, Mar 29, 2013 at 1:08 PM, Douglas N Greve
wrote:

> what are you using to do STC? I think by default FSL will move it to the
> middle slice, but there is probably a way to make take into account the
> fact that the slices are not uniform over the TR. You should contact the
> list of the software you are using to get a definative answer.
> doug
>
>
> On 03/29/2013 11:37 AM, Meryem Ayse Yucel wrote:
> > Hi,
> >
> > I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am
> > wondering when I do slice time correction does that move all slices to
> the
> > mid of TR that is 1.5 s prior in time or, it moves them to the timing of
> > the mid slice, which would be the mid of image acquisition aorund 0.6 sec
> > prior in time with respect to the end of TR.
> >
> > Thank you,
> >
> > Meryem
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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[Freesurfer] FS5.2: selxavg3-sess error

[tapsya]

Dear Doug,

I am trying to analyze fMRI data where TR = 1.2 secs. For several subjects
the analysis works as expected, but for about half of the subjects when I
try to execute the command selxavg3-sess terminates with the following
error:

"OLS Beta Pass
  run 1t= 0.0


ERROR: TR mismatch between analysis and data
analysis TR = 1.2, data TR = 1.56"

I checked the *nii header information and all indicate TR = 1.2 sec. I am
not sure why I get the error. Please advise.

Thanks!

Wishes,

Tapsya


FS-FAST version: 5.2
Machine: adapt
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Re: [Freesurfer] Set up data for longitudinal processing

[Martin Reuter]

Hi Luke,

if T1A is your first time point and T1B the second, you need to do the 
second (create a directory for each). The first is doing something very 
different, it is using both inputs for a single reconstruction, by 
averaging the inputs.


Best, Martin

On 03/28/2013 12:58 PM, lukas.sch...@ukb.uni-bonn.de wrote:


Hi folks,

sorry it's me again with a very basic question. What is the best way 
to import longitudinal data?


recon-all -i /path/T1A.nii -i /path/T1B.nii  FIRSTSUBJECT

or

recon-all -i /path/T1A.nii FIRSTSUBJECT_A
recon-all -i /path/T1A.nii FIRSTSUBJECT_B

I tend to use the second choice because otherwise I would have no idea 
how to distinguish between SUBJECT-ID and TimepointID later on in the 
processing stream.


Best whises,

Luke


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Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
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Charlestown, MA 02129

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Re: [Freesurfer] Error from mri_concat while using QDEC

[Douglas N Greve]

Do you know if that version  works outside of Virtualbox?


On 03/29/2013 03:13 PM, Tudor Popescu wrote:
> I'm running freesurfer-Linux-centos4-stable-pub-v5.1.0, on Windows XP 
> SP3, through Virtualbox 4.2.10. QDEC version is 1.4
> THanks for your help
>
> On 29 March 2013 17:33, Douglas N Greve  > wrote:
>
> If yyou just type mri_concat at the command line and nothting
> happens, then something is definitely wrong. What system are you
> running on?
>
>
>
> On 03/28/2013 04:17 PM, Tudor Popescu wrote:
>
> I tried running it by itself, to remind me of the syntax, so
> that I can do a simple concatenation to see if it works. But
> after typing mri_concat and hitting Enter, nothing happens,
> I'm just returned to the command prompt.
>
> The same happens if I type the following command, from the
> folder containing the two input files
> mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz
>
> Could this indicate something is wrong with the mri_concat
> command itself?
>
> On 28 March 2013 20:01, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
> Sorry, I've totally lost track of this thread. Are you
> able to run
> mri_concat outside of QDEC?
>
>
> On 03/28/2013 03:51 PM, Tudor Popescu wrote:
> > Still stuck with this error in my QDEC analysis attempt,
> at my wit's
> > end, could anyone help please? Thanks!
> > Tudor
> >
> > On 26 March 2013 20:35, Tudor Popescu  
> >
> > 
>  >
> > Just giving this thread a new bump, as /again /I am
> receiving this
> > error from mri_concat, upon pressing the Analyze
> button in QDEC.
> > Usual suspects are ruled out: $SUBJECTS_DIR is set
> correctly
> (and
> > includes a copy of the fsaverage folder) and all files
> included in
> > the error are at the expected path. Screenshot attached.
> >
> >
> > On 18 March 2013 11:20, Tudor Popescu
> mailto:tud...@gmail.com>
> >
> > 
>  >
> > Hi Andreas
> >
> > I don't think it's about the OS (I'm on WInXP
> SP3, 32 bit,
> > hosting Linux using Vritualbox), but about the
> environment
> > variables, even though from what I could see, I
> had them all
> > correctly set. I gave up and am just running this
> through FSL..
> >
> > Tudor
> >
> >
> > On 18 March 2013 11:13, Andreas Berger
> >  
>  >
> >  
>
>   >
> > On Friday, February 01, 2013 17:12:00 Tudor
> Popescu
> wrote:
> > > Hi Doug
> > >
> > > Strangely, the basic mri_concat command now
> worked, and
> > so did the full
> > > one. I think I initially had a "\" at the
> end of my
> > command, just after the
> > > file name, which should not have been
> there; although
> > having tried again
> > > with the backslash reinstated at the end,
> the command
> > still worked. Also,
> > > the Analyze in the QDEC GUI now completes
> without
> error
> > as well.
> > >
> > > It's quite frustrating that I still don't
> know why it
> > hasn't been working
> > > all this time, especially since I didn't
>  

Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

[Lalonde, Francois (NIH/NIMH) [E]]

Hi Jorge,

Thanks for correcting my misunderstanding.  I will include all of the subjects 
to generate the covariance estimates.  Sorry to be so concrete but in comparing 
models, for instance, 1 random effect versus 2 random effects, is the same 
design matrix, X, used for all covariance estimates, the only difference being 
that the Zcols selection is different?

Thanks for your help and patience.

--Francois

From: jorge luis mailto:jbernal0...@yahoo.es>>
Reply-To: jorge luis mailto:jbernal0...@yahoo.es>>
Date: Thursday, March 28, 2013 5:36 PM
To: Francois Lalonde mailto:flalo...@mail.nih.gov>>, 
"freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] specifying random effects in LME (Linear Mixed 
Effects models)

Hi Francois

I think that you missunderstood a point of my previous answer.  You should 
always include ALL subjects (those with 1,2,3,4... and so on repeated measures) 
in your analysis whether or not the model for the covariance includes one, two, 
three or more random effects.

What I wanted to say in my previous answer is that you should have several 
subjects with more than four longitudinal measurements in your data set to 
start thinking of using such a complicated random effects covariance matrix as 
the one determined by an lme model including three random effects.

Yes, subjects with a single measure contribute to more efficient and unbiased 
estimation of the between-subject variability.

Best
-Jorge



De: "Lalonde, Francois (NIH/NIMH) [E]" 
mailto:flalo...@mail.nih.gov>>
Para: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Enviado: Jueves 28 de marzo de 2013 16:45
Asunto: Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects 
models)

Jorge,

Thanks for the clarification.  I will try an analysis using [1 2 3] with all of 
the subjects with a minimum of 4 repeats and compare the results using the same 
analysis on all subjects with a minimum of 3 repeats.  This is worthwhile for 
us since we lose quite a few when excluding those subjects with only 3 repeats. 
 Your response also brings up the interesting point of what we can expect when 
including subjects with a single measure (I think a new feature in your 
longitudinal analysis).  I guess they would contribute to specifying group 
differences at the level of the intercept?

--Francois

From: jorge luis 
mailto:jbernal0...@yahoo.es>>>
Reply-To: jorge luis 
mailto:jbernal0...@yahoo.es>>>
Date: Wednesday, March 27, 2013 4:58 PM
To: Francois Lalonde 
mailto:flalo...@mail.nih.gov>>>,
 
"freesurfer@nmr.mgh.harvard.edu>"
 
mailto:freesurfer@nmr.mgh.harvard.edu>>>
Subject: Re: [Freesurfer] specifying random effects in LME (Linear Mixed 
Effects models)

Hi Francois

If you want to test the model with three random effects including intercept, 
time, and time*time as the random effects then you should use [1 2 3] (these 
are the columns corresponding to those covariates in X). Actually, for the 
example in the wiki page we first tested [1 2 3] but the model [1 2] was the 
best at most vertices. In general, you need more than 4 repeated measures to 
think of including three random effects in the model for the covariance. 
Otherwise two random effects are usually enough (you can still include 
time*time in the model for the mean as in the wiki ). Also, computation time 
increases quickly with the number of random effects.

There is an oncoming paper that will expand more on our longitudinal 
mass-univariate analyses with lme (hopefully soon).

Best
-Jorge




De: "Lalonde, Francois (NIH/NIMH) [E]" 
mailto:flalo...@mail.nih.gov>>>
Para: 
"freesurfer@nmr.mgh.harvard.edu>"
 
mailto:freesurfer@nmr.mgh.harvard.edu>>>
Enviado: Miércoles 27 de marzo de 2013 15:20
Asunto: [Freesurfer] specifying random effects in LME (Linear Mixed Effects 
models)

I am following the wiki page for LME analysis and I have a quick question.  The 
Mass-univariate example near the bottom of the page proposes an initial model 
that contains intercept, linear and quadratic terms as random effects.  
However, the examples just below for lme_mass_fit_EM_init(),  
lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects.  Should the

Re: [Freesurfer] More QDEC questions

[Tudor Popescu]

Thanks Doug, just to follow-up on some of these:

> - why does QDEC only provide the volume of /subcortical/
> > structures under StatsDataImport/aseg.volume, when the automatic
> > GM/WM segmentation is done for the entire brain, not just for
> > subcortical regions?
> >
> No reason in particular. You can add them into the qdec table.
>
Do you mean aseg.volume also contains the volume of cortical structures as
well, not just subcortical? If so, how can one retrieve those?

> - how are the volume measurements provided in aseg.volume
> > different from the ones done obtained with a VBM analysis?
> >
> Does VBM give segmentation volumes? I thought it was voxel-wise
> exploratory.

I was making a confusion here: in FSL, it's not FSL_VBM that gives you the
volume of a given structure, but FSLSTATS, when used with a certain
mask/ROI. My question is, then, whether the volume measurements provided in
aseg.volume are similar to what you would get with FSLSTATS, with the
exception that aseg.volume uses automatic segmentation rather than a
cutom-defined mask

> - how is a QDEC thickness analysis different from a regular
> > AN(C)OVA in which you are interested in main and interaction
> > effects of the IVs on the DV? I ask this because some of the
> > questions that appear in QDEC's Analysis Results tab – e.g. "is
> > the correlation between (DV) and (IV) different from zero?" –
> > would not (I think) be directly answerable by an ANOVA
> >
> Often times they are the same, depends on the contrast. I don't know
> what IV and DV are so I can't answer your specific question.

IV = independent variable; DV = dependent variable.
Since in QDEC you can't define the contrast vector directly (it's created
automatically, if I understand it correctly), then it seems to me that the
analysis is just an AN(C)OVA, so I still don't understand how questions
such as the one about the correlation being non-zero can be answered..

Thanks again very much Doug!!

On 28 March 2013 20:07, Douglas N Greve  wrote:

>
> On 03/28/2013 03:53 PM, Tudor Popescu wrote:
> > I was wondering if anybody is able to help with (any one of) these
> > questions? That would be really helpful, as I could not find an answer
> > on the wiki.
> >
> > Many thanks in advance!
> >
> > On 26 March 2013 20:44, Tudor Popescu  > > wrote:
> >
> > Hi everyone,
> >
> >
> > My QDEC analysis ran into an error message that seems to be a
> > "classic" (and, so far, it seems unsolved), from mri_concat, which
> > I've described in a separate message, just sent.
> >
> >
> > I have, however, more theoretical questions about QDEC, which I
> > hope some kind soul will help me with:
> >
> >
> > - why does QDEC only provide the volume of /subcortical/
> > structures under StatsDataImport/aseg.volume, when the automatic
> > GM/WM segmentation is done for the entire brain, not just for
> > subcortical regions?
> >
> No reason in particular. You can add them into the qdec table.
> >
> >
> > - how are the volume measurements provided in aseg.volume
> > different from the ones done obtained with a VBM analysis?
> >
> Does VBM give segmentation volumes? I thought it was voxel-wise
> exploratory.
> >
> > - why is /volume /the result of /segmentation /(aseg.volume)
> > whereas /thickness /derives from /parcelation
> > /(rh.aparc.thickness)? Is it not the case that both operations
> > (segmentation+parcellation) are necessary to calculate volume as
> > well as thickness?
> >
> You can get volume from parcellations too (this is supplied in the
> ?h.apac.stats file). You can't get thickness from non-surface structures
> like amygdala.
> >
> >
> > - how is a QDEC thickness analysis different from a regular
> > AN(C)OVA in which you are interested in main and interaction
> > effects of the IVs on the DV? I ask this because some of the
> > questions that appear in QDEC's Analysis Results tab – e.g. "is
> > the correlation between (DV) and (IV) different from zero?" –
> > would not (I think) be directly answerable by an ANOVA
> >
> Often times they are the same, depends on the contrast. I don't know
> what IV and DV are so I can't answer your specific question.
> >
> > - would the same type of ANOVA done by QDEC be doable by
> > extracting the values of the DV for each subject (using e.g.
> > /aseg.volume/) and then doing the ANOVA in e.g. SPSS? If so, when
> > would you do one versus the other?
> >
> Yes. QDEC is an exploratory voxel-based method so effects don't have to
> lie cleanly within an ROI boundary.
> >
> > - why is it that only continuous factors (e.g. age) can be taken
> > in the analysis as nuisance factors, when discrete variables (e.g.
> > gender) might also be irrelevant for a particular analysis and
> > thus belong to the Nuisance Factor list?
> >
> It is just a matter of convenience in 

Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

[jorge luis]

Yes, it is. You should use the same design matrix X and vary the Zcols 
selection . 

Just a note: If you find the spatiotemporal mixed effects model fitting 
procedure  described in the wiki too complicated (the paper explaining it is 
still under revision) you have the option to use the simpler vertex-wise mixed 
effects model. Something like this:

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

This will simply fit a linear mixed effects model independently at each vertex.

Best
-Jorge






>
> De: "Lalonde, Francois (NIH/NIMH) [E]" 
>Para: "freesurfer@nmr.mgh.harvard.edu"  
>Enviado: Viernes 29 de marzo de 2013 16:03
>Asunto: Re: [Freesurfer] specifying random effects in LME (Linear Mixed 
>Effects models)
> 
>Hi Jorge,
>
>Thanks for correcting my misunderstanding.  I will include all of the subjects 
>to generate the covariance estimates.  Sorry to be so concrete but in 
>comparing models, for instance, 1 random effect versus 2 random effects, is 
>the same design matrix, X, used for all covariance estimates, the only 
>difference being that the Zcols selection is different?
>
>Thanks for your help and patience.
>
>--Francois
>
>From: jorge luis mailto:jbernal0...@yahoo.es>>
>Reply-To: jorge luis mailto:jbernal0...@yahoo.es>>
>Date: Thursday, March 28, 2013 5:36 PM
>To: Francois Lalonde mailto:flalo...@mail.nih.gov>>, 
>"freesurfer@nmr.mgh.harvard.edu" 
>mailto:freesurfer@nmr.mgh.harvard.edu>>
>Subject: Re: [Freesurfer] specifying random effects in LME (Linear Mixed 
>Effects models)
>
>Hi Francois
>
>I think that you missunderstood a point of my previous answer.  You should 
>always include ALL subjects (those with 1,2,3,4... and so on repeated 
>measures) in your analysis whether or not the model for the covariance 
>includes one, two, three or more random effects.
>
>What I wanted to say in my previous answer is that you should have several 
>subjects with more than four longitudinal measurements in your data set to 
>start thinking of using such a complicated random effects covariance matrix as 
>the one determined by an lme model including three random effects.
>
>Yes, subjects with a single measure contribute to more efficient and unbiased 
>estimation of the between-subject variability.
>
>Best
>-Jorge
>
>
>
>De: "Lalonde, Francois (NIH/NIMH) [E]" 
>mailto:flalo...@mail.nih.gov>>
>Para: "freesurfer@nmr.mgh.harvard.edu" 
>mailto:freesurfer@nmr.mgh.harvard.edu>>
>Enviado: Jueves 28 de marzo de 2013 16:45
>Asunto: Re: [Freesurfer] specifying random effects in LME (Linear Mixed 
>Effects models)
>
>Jorge,
>
>Thanks for the clarification.  I will try an analysis using [1 2 3] with all 
>of the subjects with a minimum of 4 repeats and compare the results using the 
>same analysis on all subjects with a minimum of 3 repeats.  This is worthwhile 
>for us since we lose quite a few when excluding those subjects with only 3 
>repeats.  Your response also brings up the interesting point of what we can 
>expect when including subjects with a single measure (I think a new feature in 
>your longitudinal analysis).  I guess they would contribute to specifying 
>group differences at the level of the intercept?
>
>--Francois
>
>From: jorge luis 
>mailto:jbernal0...@yahoo.es>>>
>Reply-To: jorge luis 
>mailto:jbernal0...@yahoo.es>>>
>Date: Wednesday, March 27, 2013 4:58 PM
>To: Francois Lalonde 
>mailto:flalo...@mail.nih.gov>>>,
> 
>"freesurfer@nmr.mgh.harvard.edu>"
> 
>mailto:freesurfer@nmr.mgh.harvard.edu>>>
>Subject: Re: [Freesurfer] specifying random effects in LME (Linear Mixed 
>Effects models)
>
>Hi Francois
>
>If you want to test the model with three random effects including intercept, 
>time, and time*time as the random effects then you should use [1 2 3] (these 
>are the columns corresponding to those covariates in X). Actually, for the 
>example in the wiki page we first tested [1 2 3] but the model [1 2] was the 
>best at most vertices. In general, you need more than 4 repeated measures to 
>think of including three random effects in the model for the covariance. 
>Otherwise two random effects are usually enough (you can still include 
>time*time in the model for the mean as in the wiki ). Also, computation time 
>increases quickly with the number of random effects.
>
>There is an oncoming paper that will expand more on our longitudinal 
>mass-univariate analyses with lme (hopefully soon).
>
>Best
>-Jorge
>
>
>
>
>De: "Lalonde, Francois (NIH/NIMH) [E]"