Re: [Freesurfer] recon-all with FLAIR error no FSL installed

[Bruce Fischl]

If the FLAIR was acquired in the same session you might be ok, as 
bbregister inititialized from the headers will be close enough unless there 
is large-scale movement between scans.

Bruce


On Tue, 28 May 2013, Popescu, Veronica wrote:


Dear all,
How "fatal" is the FSL environment not being initialized for FreeSurfer 5.3 
with FLAIR refinement?
I do get results (which look good).
Should I rerun them with FSL installed?
Thank you very much in advance!
Sincerely,
Veronica


-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: maandag 27 mei 2013 14:19
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] recon-all with FLAIR error no FSL installed

Hi Veronica

thanks for the offer, but I don't need to see them. Glad it seems to be
working. As for BBR, I'll leave that for Doug
Bruce
On Mon, 27 May 2013, Popescu,
Veronica wrote:


Dear Bruce,
They look good to me. Should I upload a couple of them, so you can have a look? 
They're about 230MB each.
My question is: how serious is the BBR not initializing? Should I run 
everything again with FSL installed?
Best wishes,
Veronica

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: vrijdag 24 mei 2013 15:59
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed

Hi Veronica

BBR can use FSL or SPM to initialize, although we'll probably add an option
in the future to use some things that Martin Reuter and Christian Wachinger
are working on. How did the refinement work? We've only run it on a handful
of cases, so it's pretty bleeding edge and I'm interested in feedback.

cheers
Bruce


On Fri, 24 May 2013, Popescu, Veronica
wrote:


Dear all,
I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. 
I do get results but there's an
error message in the log file (attached) about the FSL installation missing.  
How bad is it? Do I have to rerun everything with FSL installed? And if so, is 
there any version that is
preferable?
Thank you very much in advance!
Best wishes,
Veronica
 





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Re: [Freesurfer] rerun interrupted processes

[Bruce Fischl]

Hi Valeria

can you address this type of question to the list so that others can 
answer and learn from the answers? Yes, you can run

recon-all -make all -s 

and it should pick up from where it left off
Bruce


On Tue, 28 May 2013, Valeria Contarino 
wrote:

> Dear Bruce,
> I have a new question for you.
> I was running 30 subjects when processes were interrupted because of no more 
> space left on device.
> Do I have the chance for starting again the processes from where they stopped?
> 
> Thank you.
> 
> Regards,
> Valeria
> 
>
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Re: [Freesurfer] fix talairach transform

[Bruce Fischl]

Hi Laouchedi

these alignments look fine. I am a bit concerned at how dark your images 
are near the top of the head. What coil are you using? This is probably 
why you are having trouble.


cheers
Bruce
On Tue, 28 May 2013, LAOUCHEDI MAKHLOUF wrote:


Hi
    i have a problem when running "recon-all -all", so i decided to split the 
process into three staps :
"recon-all -autorecon1", ""recon-all -autorecon2" and "recon-all -autorecon3". 
i have just finished with the
first step (recon-all -autorecon1) and looked for misalignment in talairach 
transform for all subjects using
"tkregister2 --mgz --s ctr1 --fstal"  (i can't use "--surf orig " because i 
haven't the surfaces yet). so i
used the small red cross in the coronal, sagittal and axial views to align as 
much as possible. my goal is to
extract the cortical labels (cortical parcellation). is it necessary to have a 
precise talairach transform just
for this purpose ?

Thank you

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Re: [Freesurfer] BBR Register failing

[Douglas N Greve]

and bbregister?

On 05/28/2013 02:03 AM, Salil Soman wrote:
> It was attached to my earlier email (included again here). The only 
> chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo 
> "FSVOL $fsvol").
>
> -S
>
>
>
> On Mon, May 27, 2013 at 9:14 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Can you send me your original version of fslregister and bregister?
>
>
> On 5/27/13 10:53 PM, Salil Soman wrote:
>> I have been using 5.3 of freesurfer for centos 6. As far as I can
>> tell, the problem was with fslregister, which was getting called
>> by bbregister. I've downloaded the link you just sent, remarked
>> out the line I added to fslregister (see the file I sent in
>> response to your email), and I get the same error. Restoring my
>> modification makes the code work again.
>>
>> Thank you,
>>
>> Sal
>>
>>
>> On Mon, May 27, 2013 at 7:43 PM, Douglas Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> which version of FS are you using? This was a problem with
>> 5.2 but it should be fixed with 5.3.
>> If you have 5.2 or earlier, you can use this version of
>> bbregister
>> 
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
>>
>> doug
>>
>>
>> On 5/27/13 10:32 PM, Salil Soman wrote:
>>> Thank you Doug,
>>>
>>> fsvol was defined, which was why I was confused. I put in a
>>> command to echo the fsvol value in the line before where the
>>> error was getting generated, and it echoed "ERROR". Adding a
>>> line specifically defining fsvol using set in the section
>>> fixed the problem (as far as I can tell).
>>>
>>> -Sal
>>>
>>>
>>> On Mon, May 27, 2013 at 7:16 PM, Douglas Greve
>>> >> > wrote:
>>>
>>> Hi Sal, fsvol should be defined. Can you send me your
>>> fslregister?
>>> doug
>>>
>>>
>>>
>>> On 5/26/13 12:58 AM, Salil Soman wrote:
 Dear Freesurfer experts,

 WIth the combination of FS 5.3 and FSL 5.0.2.1, It
 looks like I am having some problems with the
 fslregister script. From what I have been able to
 investigate. It looks like there is an issue that fsvol
 may not get named if you are not dealing .cor files.

 Code in question from fslregister script:

 # Use the rawavg as input (for testing only)
 if($fsvol == rawavg.cor) then
   set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz
   if(! -e $refvol) then
 # Does not exist, create
 set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz
 set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz
 set cmd = (mri_vol2vol --mov $rawavg --targ $orig
 --o $refvol \
 --no-save-reg --regheader)
 echo $cmd |& tee -a $LF
 $cmd |& tee -a $LF
 if($status) exit 1;
 # Now mask it
 set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz
 set cmd = (mri_mask $refvol $brain $refvol)
 echo $cmd |& tee -a $LF
 $cmd |& tee -a $LF

 I think this lack of fsvol being named results in the
 errors I am getting:

 --
 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
 mri_convert ERROR: could not determine file for
 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
 ./tmp.bbregister.756/fslregister/refvol.fslregister.nii
 mri_convert ERROR: could not determine file for
 /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
 ./tmp.bbregister.756/fslregister/refvol.fslregister.nii

 mri_convert: extra arguments ("not" and following)

 Any suggestions would be a huge help.

 -Sal




 On Sat, May 25, 2013 at 8:35 PM, Salil Soman
 mailto:salso...@stanford.edu>>
 wrote:

 Done. Thank you for your consideration. The best I
 can figure so far is
 1) the script's attempt to make the
 tmp.bbregister.7392 directory fails
 and 2) (after I manually make this directory),
 there seems to be something going wrong at the
 level of fslregister

 I have fsl 5.0.2.1 and freesurfer 5.3 running, and
 am regularly able

Re: [Freesurfer] minor bug report

[Douglas N Greve]

This is an annoying mismatch between linux and osx.



On 05/25/2013 11:09 PM, Joseph Dien wrote:
> when I run: isxconcat-sess -sf sessidlist.dat -analysis CPA.sm05.lh 
> -all-contrasts -o secondLevel
>
> I get the error messages:
>
> secondLevel/CPA.sm05.mni305/log/isxconcat.log
>
> stat: illegal option -- c
>
> usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...]
>
> stat: illegal option -- c
>
> usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...]
>
> stat: illegal option -- c
>
> usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file …]
>
> ...
>
>
> I'm assuming this isn't a serious problem as it just seems to affect 
> what goes into the log file but thought you might want to know.
> This is on OS X 10.8.2 with Freesurfer 5.2.0.
>
> Cheers!
>
> Joe
>
> 
>
> Joseph Dien,
> Senior Research Scientist
> University of Maryland
>
> E-mail: jdie...@mac.com 
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://joedien.com//
>
>
>
>
>
>
>
>
>
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] area measurements FS5.1

[Benjamín Garzón]

Hi,

I have processed a sample with FS 5.1 and would like to do a group 
analysis of surface-based area.

According to the release notes ( ** ) there is an issue with the 
conversion into standard space. I found a former post pointing to a 
version of preproc-sess that to my understanding should fix that, but 
the file is not there any more. Is there any quick fix for this problem 
without having to move to 5.3 / could I get that file?

Thanks,

Benjamin


** There is a bug in the way that FS converts surface-based area (eg, 
lh.area) and volume (eg, lh.volume) into standard space. The files 
themselves are fine, it is the way they are transfered to standard space 
that is the problem. You will not need to re-analyze any of your 
individual subject data. The volumes of the subcortical structures are 
unaffected by this problem. Global measures of cortical volume are also 
unaffected.




-- 
Benjamín Garzón, Ph.D.

Karolinska Institutet
Department of Neuroscience
Retzius Väg 8
17177 Stockholm (SWEDEN)

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[Freesurfer] nuintensitycor and skullstrip problems

[LAOUCHEDI MAKHLOUF]

hi 
  i send you the rawavg.mgz of the subject with the massive artefact. i inform 
you that i proceeded differently by splitting the recon-all -all into three 
steps (as in freesurfer wiki) : (1) recon-all -autorecon1, (2) recon-all 
-autorecon2 (3)  recon-all -autorecon3. i just finished with the first step 
which still didn't work for some subjects so i deleted then in my SUBJECTS_DIR 
then i run "recon-all -i" to regenerate them. after that i re-run "recon-all 
-autorecon1" and it worked even for the subject with the artefacted rawavg.mgz 
i am sending you.
 

   i noticed also that some extra cerebral structures like dura is not fully 
removed after the skullstripping step, and i reviewed some of my previous 
datasets i processed with freesurfer and i noticed that the cortical
 ribbon (containing the cortical parcellation) fits well the gray matter. so is 
a wise idea to not bother a lot about these "some" extra cerebral structures 
left and just go forward with the rest of the recon-all pipeline (but of course 
i'll take a look a posteriori).

Thanks
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Re: [Freesurfer] area measurements FS5.1

[Douglas N Greve]

try that link again
doug

On 05/28/2013 10:16 AM, Benjamín Garzón wrote:
> Hi,
>
> I have processed a sample with FS 5.1 and would like to do a group
> analysis of surface-based area.
>
> According to the release notes ( ** ) there is an issue with the
> conversion into standard space. I found a former post pointing to a
> version of preproc-sess that to my understanding should fix that, but
> the file is not there any more. Is there any quick fix for this problem
> without having to move to 5.3 / could I get that file?
>
> Thanks,
>
> Benjamin
>
>
> ** There is a bug in the way that FS converts surface-based area (eg,
> lh.area) and volume (eg, lh.volume) into standard space. The files
> themselves are fine, it is the way they are transfered to standard space
> that is the problem. You will not need to re-analyze any of your
> individual subject data. The volumes of the subcortical structures are
> unaffected by this problem. Global measures of cortical volume are also
> unaffected.
>
>
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] nuintensitycor and skullstrip problems

[Bruce Fischl]

can you send me the whole .mgz volume? And your recon-all command line that 
fails?


On Tue, 28 May 2013, LAOUCHEDI 
MAKHLOUF wrote:



hi
  i send you the rawavg.mgz of the subject with the massive artefact. i inform 
you that i proceeded differently by splitting the
recon-all -all into three steps (as in freesurfer wiki) : (1) recon-all 
-autorecon1, (2) recon-all -autorecon2 (3) recon-all
-autorecon3. i just finished with the first step which still didn't work for 
some subjects so i deleted then in my SUBJECTS_DIR
then i run "recon-all -i" to regenerate them. after that i re-run "recon-all 
-autorecon1" and it worked even for the subject
with the artefacted rawavg.mgz i am sending you.

   i noticed also that some extra cerebral structures like dura is not fully 
removed after the skullstripping step, and i
reviewed some of my previous datasets i processed with freesurfer and i noticed 
that the cortical ribbon (containing the
cortical parcellation) fits well the gray matter. so is a wise idea to not bother a lot 
about these "some" extra cerebral
structures left and just go forward with the rest of the recon-all pipeline 
(but of course i'll take a look a posteriori).

Thanks

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Re: [Freesurfer] mri_anatomical_stats segmentation fault

[Douglas N Greve]

Rob, can you send me your label?

doug

On 05/27/2013 01:00 PM, Rob Tennyson wrote:
> Hi All,
>
> I'm running "mris_anatomical_stats" with a few manually defined 
> labels. For a few of my subjects, I am getting the error: 
> "Segmentation fault" on one of the labels. However, the other manually 
> defined labels process without any errors on these same subjects.
>
> For example, I am running "mri_anatomical_stats" on subject 33_bay6 
> with a manually defined ERC label, a manually defined PHC label, and a 
> manually defined medial frontal gyrus label. The only label that runs 
> an error for this subject is the PHC label. This PHC label runs 
> without any errors on the rest of my subjects.
>
> Here is what is displayed when running a label that fails:
>
> "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 
> 33_bay6 lh
> limiting computations to label lh.PHC_1.label.
> reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz...
> reading input surface 
> /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
> reading input pial surface 
> /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial...
> reading input white surface 
> /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
> Segmentation fault"
>
> Does anyone know what may be causing the Segmentation fault and what 
> steps I should take to fix it?
>
> Thank you for your help!
> Rob
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] mris_resample: Command not found.

[Barron, Daniel S]

Hello,

I am trying to perform an inter-subject registration using mri_cvs_register on 
version 5.3.

When I ran mri_cvs_check, my feedback was I needed to find 
"mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html

mri_cvs_register kicks off well, but eventually it ends with:

"mris_resample: Command not found."

I go into my $FREESURFER_HOME/bin directory and note that mris_resample is 
truly not there.  Did I not install 5.3 properly?

I have attached a log file in case this helps.

Cheers,
Daniel




MLL_to_MNI152_T1_1mm.mri_cvs_register.1305241528.log
Description: MLL_to_MNI152_T1_1mm.mri_cvs_register.1305241528.log
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Re: [Freesurfer] command not found

[clelia pellicano]

Hi,

I have tried :

>> setenv FREESURFER_HOME /Applications/freesurfer
 >> source $FREESURFER_HOME/SetUpFreesurfer.csh
 >> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz

I got this message:

dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
  Referenced from: /Applications/freesurfer/bin/qdec.bin
  Reason: image not found
Trace/BPT trap

I checked online and found here how to do. It was a problem with XQuartz.

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


Now it is working.

Thank you,

Clelia



On Fri, May 24, 2013 at 7:26 PM, Z K  wrote:

> Clelia,
>
> Please type the following commands in the terminal window and provide us
> any error message you may receive.
>
>  >> setenv FREESURFER_HOME /Applications/freesurfer
>  >> source $FREESURFER_HOME/SetUpFreesurfer.csh
>  >> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz
>
> If a window with an image pops open than freesurfer is installed and
> ready to go. If not than please provide whatever error message you may
> receive.
>
> -Zeke
>
>
> On 05/24/2013 12:15 PM, clelia pellicano wrote:
> > Hi Louise,
> > yes, teh FreeSurfer related commands are still not found. The other
> > thing is that I had problem with license file. I have created a file in
> > Applications/Freesurfer named .license and tried to copy inside le
> > license key but I'm not sure that it worked beacuse if I write cd
> > .license I get 'it is not a file not a directory'.
> > Thanks
> > Clelia
> >
> > On Fri, May 24, 2013 at 5:09 PM, Louis Nicholas Vinke
> > mailto:vi...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Clelia,
> > That mv command is failing presumably because SetUpFreeSurfer.txt
> > does not exist in that directory.  What are you trying to do with
> > the mv command?
> >
> > It does look like freesurfer was sourced successfully.  Are the
> > FreeSurfer related commands still not found?
> >
> > Don't forget to cc the freesurfer mailing list.
> >
> > -Louis
> >
> > On Fri, 24 May 2013, clelia pellicano wrote:
> >
> > Hi Louise,
> > I'm now using tcsh. Here what I did
> >
> >[dyn1097-8:~] cpellica% setenv FREESURFER_HOME
> > /Applications/freesurfer
> > [dyn1097-8:~] cpellica% source
> > /Applications/freesurfer/__SetUpFreesurfer.csh
> >  freesurfer-Darwin-lion-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
> > FSL_DIR   /usr/local/fsl
> > [dyn1097-8:~] cpellica% mv  SetUpFreeSurfer.txt
> SetUpFreeSurfer.csh
> > mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such
> > file or directory
> >
> > Do you have any advice?
> >
> > Thanks
> >
> > Clelia
> >
> >
> >
> >
> >
> > On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke
> > mailto:vi...@nmr.mgh.harvard.edu>>
> > wrote:
> >Hi Clelia,
> >What do you run to source FS and do you get any output in
> > your terminal after doing so?  What operating system are
> >you running?  You might try using c-shell instead of bash.
> >-Louis
> >
> >On Fri, 24 May 2013, clelia pellicano wrote:
> >
> >  Hi Louis,
> >  thank you for your answer.
> >  I sourced freesurfer again, but I still  get
> > 'command not found'.
> >  What can I try?
> >  Thank you,
> >
> >  Clelia
> >
> >
> >  On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas
> > Vinke  > > wrote:
> >Hi Clelia,
> >If this is in a new terminal then you'll have
> > to source freesurfer again. See here for details:
> > https://surfer.nmr.mgh.__harvard.edu/fswiki/__SetupConfiguration
> > 
> >-Louis
> >
> >On Wed, 22 May 2013, clelia pellicano wrote:
> >
> >  Hi,
> >  I have run recon-all -s bert -all to
> > try my installation and it worked.
> >  Now, when I try to use other command
> > (and also again recon-all -s bert -all) I always get
> >  this:
> >
> >  dyn1097-8:subjects cpellica$ tkmedit
> > bert orig.mgz
> >  -bash: tkmedit: command not found
> >  

Re: [Freesurfer] BBR Register failing

[Douglas N Greve]

I know, but I want to see what version of bbregister you are using
On 05/28/2013 10:29 AM, Salil Soman wrote:
>
> I did not make any changes to bbregister.
>
> Thank you for all your help.
>
> Sal
>
> On May 28, 2013 6:57 AM, "Douglas N Greve"  > wrote:
>
> and bbregister?
>
> On 05/28/2013 02:03 AM, Salil Soman wrote:
>
> It was attached to my earlier email (included again here). The
> only chnages I made are at lines 129 (set fsvol = brainmask)
> and 132 (echo "FSVOL $fsvol").
>
> -S
>
>
>
> On Mon, May 27, 2013 at 9:14 PM, Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> Can you send me your original version of fslregister and
> bregister?
>
>
> On 5/27/13 10:53 PM, Salil Soman wrote:
>
> I have been using 5.3 of freesurfer for centos 6. As
> far as I can
> tell, the problem was with fslregister, which was
> getting called
> by bbregister. I've downloaded the link you just sent,
> remarked
> out the line I added to fslregister (see the file I
> sent in
> response to your email), and I get the same error.
> Restoring my
> modification makes the code work again.
>
> Thank you,
>
> Sal
>
>
> On Mon, May 27, 2013 at 7:43 PM, Douglas Greve
>  
>  >> wrote:
>
>
> which version of FS are you using? This was a
> problem with
> 5.2 but it should be fixed with 5.3.
> If you have 5.2 or earlier, you can use this
> version of
> bbregister
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister
>
> doug
>
>
> On 5/27/13 10:32 PM, Salil Soman wrote:
>
> Thank you Doug,
>
> fsvol was defined, which was why I was
> confused. I put in a
> command to echo the fsvol value in the line
> before where the
> error was getting generated, and it echoed
> "ERROR". Adding a
> line specifically defining fsvol using set in
> the section
> fixed the problem (as far as I can tell).
>
> -Sal
>
>
> On Mon, May 27, 2013 at 7:16 PM, Douglas Greve
>  
>  >> wrote:
>
> Hi Sal, fsvol should be defined. Can you
> send me your
> fslregister?
> doug
>
>
>
> On 5/26/13 12:58 AM, Salil Soman wrote:
>
> Dear Freesurfer experts,
>
> WIth the combination of FS 5.3 and FSL
> 5.0.2.1, It
> looks like I am having some problems
> with the
> fslregister script. From what I have
> been able to
> investigate. It looks like there is an
> issue that fsvol
> may not get named if you are not
> dealing .cor files.
>
> Code in question from fslregister script:
>
> # Use the rawavg as input (for testing
> only)
> if($fsvol == rawavg.cor) then
>   set refvol =
> $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz
>   if(! -e $refvol) then
> # Does not exist, create
> set orig =
> $SUBJECTS_DIR/$subjid/mri/orig.mgz
> set rawavg =
> $SUBJECTS_DIR/$subjid/mri/rawavg.mgz
> set cmd = (mri_vol2vol --mov
> $rawavg --targ $orig
> --o $refvol \
> --no-save-reg --regheader)
> echo $cmd |& tee -a $LF
> $cmd |& tee -a $LF
> if($status)

Re: [Freesurfer] mris_resample: Command not found.

[Lilla Zollei]

Hi Daniel,

What operating system are you using?

Lilla

On Tue, 28 May 2013, Barron, Daniel S wrote:


Hello,

I am trying to perform an inter-subject registration using mri_cvs_register on 
version 5.3. 

When I ran mri_cvs_check, my feedback was I needed to find 
"mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html

mri_cvs_register kicks off well, but eventually it ends with:

"mris_resample: Command not found."

I go into my $FREESURFER_HOME/bin directory and note that mris_resample is 
truly not there.  Did I not install 5.3 properly? 

I have attached a log file in case this helps.

Cheers,
Daniel



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Re: [Freesurfer] mri_anatomical_stats segmentation fault

[Douglas N Greve]

Nothing looks like it is wrong with that label. Can you verify that the 
white surface has not been changed since the label was created? Check 
how many vertices the white surface has with mris_info. The PHC label 
references a vertex index as high as 163798. If the white surface does 
not have that many veritices, then that could cause the problem.
doug


On 05/28/2013 10:33 AM, Rob Tennyson wrote:
> Hi Doug,
>
> Attached are the three labels I'm having an issue with (each with a 
> different subject). These are built from areas that we found 
> functional differences between a healthy control group and a MDD 
> group. I was going to take a look at the anatomical stats to see if 
> there are thickness or volume differences as well.
>
> I am also going to review the white surface soon as Bruce suggested.
>
>
> On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Rob, can you send me your label?
>
> doug
>
> On 05/27/2013 01:00 PM, Rob Tennyson wrote:
> > Hi All,
> >
> > I'm running "mris_anatomical_stats" with a few manually defined
> > labels. For a few of my subjects, I am getting the error:
> > "Segmentation fault" on one of the labels. However, the other
> manually
> > defined labels process without any errors on these same subjects.
> >
> > For example, I am running "mri_anatomical_stats" on subject 33_bay6
> > with a manually defined ERC label, a manually defined PHC label,
> and a
> > manually defined medial frontal gyrus label. The only label that
> runs
> > an error for this subject is the PHC label. This PHC label runs
> > without any errors on the rest of my subjects.
> >
> > Here is what is displayed when running a label that fails:
> >
> > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b
> > 33_bay6 lh
> > limiting computations to label lh.PHC_1.label.
> > reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz...
> > reading input surface
> > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
> > reading input pial surface
> > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial...
> > reading input white surface
> > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
> > Segmentation fault"
> >
> > Does anyone know what may be causing the Segmentation fault and what
> > steps I should take to fix it?
> >
> > Thank you for your help!
> > Rob
> >
> >
> > ___
> > 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.
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] area measurements FS5.1

[Benjamín Garzón]

Thanks, Doug.
I guess it's the mris_preproc file there what I need, not preproc-sess...
Does this version do the areal interpolation as described in Winkler 
2012 'Measuring and comparing brain cortical surface area and other 
areal quantities 
'?


Best regards, Benjamin

On 05/28/2013 04:16 PM, Benjamín Garzón wrote:

Hi,

I have processed a sample with FS 5.1 and would like to do a group 
analysis of surface-based area.


According to the release notes ( ** ) there is an issue with the 
conversion into standard space. I found a former post pointing to a 
version of preproc-sess that to my understanding should fix that, but 
the file is not there any more. Is there any quick fix for this 
problem without having to move to 5.3 / could I get that file?


Thanks,

Benjamin


** There is a bug in the way that FS converts surface-based area (eg, 
lh.area) and volume (eg, lh.volume) into standard space. The files 
themselves are fine, it is the way they are transfered to standard 
space that is the problem. You will not need to re-analyze any of your 
individual subject data. The volumes of the subcortical structures are 
unaffected by this problem. Global measures of cortical volume are 
also unaffected.








--
Benjamín Garzón, Ph.D.

Karolinska Institutet
Department of Neuroscience
Retzius Väg 8
17177 Stockholm (SWEDEN)

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Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?

[Gunter, Geoffrey]

Thanks for your response, Douglas.

I tried your suggestion, it doesn't appear to have changed the transformation 
at all though. There is still no scaling being applied to the surface.

Is there anything else I can try to fix this problem?

Thanks,
Geoff

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 24, 2013 5:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf 
not scaling properly?

Try

mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg rawavg.mgz
--tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6


On 05/24/2013 04:42 PM, Gunter, Geoffrey wrote:
> Hello,
>
> I'm trying to resample Freesurfer output volumes and surfaces back
> into their native anatomical space using mri_vol2vol and
> mri_surf2surf. The volumes appear to be resampled correctly, their
> resolution and orientation match the original images'.
>
> However, the resampled surfaces do not appear to have been transformed
> correctly by mri_surf2surf. When I visually compare them to the
> Freesurfer-space surfaces overlaid on the brain images in FreeView,
> TKMEdit, Paraview-CAWorks, etc., they seem to be identical to the
> un-transformed, Freesurfer-space surfaces. In addition, when I check
> the list of vertices for transformed and untransformed surfaces, the
> coordinates of each vertex are unchanged.
>
> These are the commands that I'm using:
>
> mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o
> resamp_brain.mgz
>
> mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg --tval
> resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6
>
> The registration file, "resamp_brain.mgz.reg" looks like this:
>
> subject-unknown
> 0.937500
> 0.937500
> 1.00
> 1.000e+00 0.000e+00 0.000e+00
> 0.000e+00
> 0.000e+00 1.000e+00 0.000e+00
> 0.000e+00
> 0.000e+00 0.000e+00 1.000e+00
> 0.000e+00
> 0 0 0 1
> round
>
> My Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> Could it be that mri_surf2surf is not applying scaling transformations
> correctly?
>
> Thanks for your help,
> Geoff
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] area measurements FS5.1

[Douglas N Greve]

We don't have an implementation of Anderson's code that we are 
releasing. mris_preproc (not preproc-sess) has a mechanism to perform 
areal interpolation that is not as good as Anderson's, but it is what we 
have.
doug



On 05/28/2013 11:19 AM, Benjamín Garzón wrote:
> Thanks, Doug.
> I guess it's the mris_preproc file there what I need, not preproc-sess...
> Does this version do the areal interpolation as described in Winkler 
> 2012 'Measuring and comparing brain cortical surface area and other 
> areal quantities 
> '?
>
> Best regards, Benjamin
>
> On 05/28/2013 04:16 PM, Benjamín Garzón wrote:
>> Hi,
>>
>> I have processed a sample with FS 5.1 and would like to do a group 
>> analysis of surface-based area.
>>
>> According to the release notes ( ** ) there is an issue with the 
>> conversion into standard space. I found a former post pointing to a 
>> version of preproc-sess that to my understanding should fix that, but 
>> the file is not there any more. Is there any quick fix for this 
>> problem without having to move to 5.3 / could I get that file?
>>
>> Thanks,
>>
>> Benjamin
>>
>>
>> ** There is a bug in the way that FS converts surface-based area (eg, 
>> lh.area) and volume (eg, lh.volume) into standard space. The files 
>> themselves are fine, it is the way they are transfered to standard 
>> space that is the problem. You will not need to re-analyze any of 
>> your individual subject data. The volumes of the subcortical 
>> structures are unaffected by this problem. Global measures of 
>> cortical volume are also unaffected.
>>
>>
>>
>>
>
>
> -- 
> Benjamín Garzón, Ph.D.
>
> Karolinska Institutet
> Department of Neuroscience
> Retzius Väg 8
> 17177 Stockholm (SWEDEN)
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?

[Douglas N Greve]

The problem is with the way you are creating the registration matrix, 
use this instead

tkregister2 --mov rawavg.mgz --targ orig.mgz --regheader --noedit --reg  
resamp_brain.mgz.reg

doug




On 05/28/2013 11:19 AM, Gunter, Geoffrey wrote:
> Thanks for your response, Douglas.
>
> I tried your suggestion, it doesn't appear to have changed the transformation 
> at all though. There is still no scaling being applied to the surface.
>
> Is there anything else I can try to fix this problem?
>
> Thanks,
> Geoff
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, May 24, 2013 5:35 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf 
> not scaling properly?
>
> Try
>
> mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg rawavg.mgz
> --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6
>
>
> On 05/24/2013 04:42 PM, Gunter, Geoffrey wrote:
>> Hello,
>>
>> I'm trying to resample Freesurfer output volumes and surfaces back
>> into their native anatomical space using mri_vol2vol and
>> mri_surf2surf. The volumes appear to be resampled correctly, their
>> resolution and orientation match the original images'.
>>
>> However, the resampled surfaces do not appear to have been transformed
>> correctly by mri_surf2surf. When I visually compare them to the
>> Freesurfer-space surfaces overlaid on the brain images in FreeView,
>> TKMEdit, Paraview-CAWorks, etc., they seem to be identical to the
>> un-transformed, Freesurfer-space surfaces. In addition, when I check
>> the list of vertices for transformed and untransformed surfaces, the
>> coordinates of each vertex are unchanged.
>>
>> These are the commands that I'm using:
>>
>>  mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o
>>  resamp_brain.mgz
>>
>>  mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg --tval
>>  resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6
>>
>> The registration file, "resamp_brain.mgz.reg" looks like this:
>>
>>  subject-unknown
>>  0.937500
>>  0.937500
>>  1.00
>>  1.000e+00 0.000e+00 0.000e+00
>>  0.000e+00
>>  0.000e+00 1.000e+00 0.000e+00
>>  0.000e+00
>>  0.000e+00 0.000e+00 1.000e+00
>>  0.000e+00
>>  0 0 0 1
>>  round
>>
>> My Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>>
>> Could it be that mri_surf2surf is not applying scaling transformations
>> correctly?
>>
>> Thanks for your help,
>> Geoff
>>
>>
>> ___
>> 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.
>
>
>
>
>

-- 
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
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Re: [Freesurfer] mris_resample: Command not found.

[Barron, Daniel S]

Hi Lilla, 
I'm using OSX 10.8.3
Thanks,
Daniel

From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 28, 2013 10:04 AM
To: Barron, Daniel S
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: mris_resample: Command not found.

Hi Daniel,

What operating system are you using?

Lilla

On Tue, 28 May 2013, Barron, Daniel S wrote:

> Hello,
>
> I am trying to perform an inter-subject registration using mri_cvs_register 
> on version 5.3.
>
> When I ran mri_cvs_check, my feedback was I needed to find 
> "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's 
> post: 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html
>
> mri_cvs_register kicks off well, but eventually it ends with:
>
> "mris_resample: Command not found."
>
> I go into my $FREESURFER_HOME/bin directory and note that mris_resample is 
> truly not there.  Did I not install 5.3 properly?
>
> I have attached a log file in case this helps.
>
> Cheers,
> Daniel
>
>
>
>


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Re: [Freesurfer] mris_resample: Command not found.

[Z K]

Hello Daniel,

This is a confirmed issue with the 64bit Mac build. A patch to fix the 
issue will be available shortly (~hours). I will email the list and you 
personally once it is available. Sorry for the inconvenience.

-Zeke

On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
> Hi Lilla,
> I'm using OSX 10.8.3
> Thanks,
> Daniel
> 
> From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu]
> Sent: Tuesday, May 28, 2013 10:04 AM
> To: Barron, Daniel S
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: mris_resample: Command not found.
>
> Hi Daniel,
>
> What operating system are you using?
>
> Lilla
>
> On Tue, 28 May 2013, Barron, Daniel S wrote:
>
>> Hello,
>>
>> I am trying to perform an inter-subject registration using mri_cvs_register 
>> on version 5.3.
>>
>> When I ran mri_cvs_check, my feedback was I needed to find 
>> "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's 
>> post: 
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html
>>
>> mri_cvs_register kicks off well, but eventually it ends with:
>>
>> "mris_resample: Command not found."
>>
>> I go into my $FREESURFER_HOME/bin directory and note that mris_resample is 
>> truly not there.  Did I not install 5.3 properly?
>>
>> I have attached a log file in case this helps.
>>
>> Cheers,
>> Daniel
>>
>>
>>
>>
>
>
> 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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>
>
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[Freesurfer] LME toolbox - univariate

[Yolanda Vives]

Dear FreeSurfer experts,

I am trying to use the LME toolbox to analyse the hippocampal change over
time in a group and also among 2 groups (2 scans per subject).

When I estimate the parameters with lme_fit_FS I become a warning saying
that the matrix is singular and my results are NaN. I guess that my design
matrix X is not correct, can you please help me?

I have followed the example from the wiki. My model for the two groups
study is the following:

Yij = ß1 + ß2*tij +ß3*Group1 + ß4*Group1 *tij + ß5*Group2 + ß6*Group2 *tij+ ß
7*Genderi + ß8*Agei + ß9*ICVi + b1i + b2i*tij + eij

1) intercept (all ones)

2) time (tij) . Here I have 0s for the first scan of each subject and a
number in years for the second scans. Is it correct?

3) one for Group1 and zero otherwise

4) colum 3) .* time

5) one for Group2 and zero otherwise

6) colum 5) .* time

7) Gender

8) Age of the subject at each scan moment.

9) ICV (converted to liters).

Thank you in advance,
Yolanda
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[Freesurfer] mri_anatomical_stats on custom 'thickness' file

[Martijn Steenwijk]

Dear all,

I've created a custom '.mgh' file containing values on the cortical surface
using mri_vol2surf. I would like to compute some statistics on this surface
in the aparc-areas computed by freesurfer. Can I then just use
 mri_anatomical_stats with option -t specifying the custom mgh file as
'thickness' input? Or does mri_anatomical_stats something more complex than
just averaging the values inside each region?

Best,
Martijn
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Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

[Douglas N Greve]

I would use mri_segstats and specify the --annot option
doug


On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
> Dear all,
>
> I've created a custom '.mgh' file containing values on the cortical 
> surface using mri_vol2surf. I would like to compute some statistics on 
> this surface in the aparc-areas computed by freesurfer. Can I then 
> just use  mri_anatomical_stats with option -t specifying the custom 
> mgh file as 'thickness' input? Or does mri_anatomical_stats something 
> more complex than just averaging the values inside each region?
>
> Best,
> Martijn
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

what is is labled?
On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote:
> Hi Doug:
>
>I use the instructions that you told me... But, why I get the gray
> colored region (red arrow) ?...
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
>
>
>> Message: 15
>> Date: Mon, 27 May 2013 22:41:41 -0400
>> From: Douglas Greve 
>> Subject: Re: [Freesurfer] white matter volume per lobe...
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> you will need to run mri_annotation2label and specify the output to be
>> an annotation file instead of a segmentation. Then you will have to run
>> mri_aparc2aseg, specifying your lobes annotation as well as --labelwm
>> (look in the recon-all.log file for an example of how wmparc.mgz is
>> created). Then run mri_segstats (you can also get an example from the
>> recon-all.log file).
>> doug
> --
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl

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

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

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Re: [Freesurfer] white matter volume per lobe...

[Gonzalo Rojas Costa]

Hi Doug:

  It is labeled as wm-rh-fusiform and wm-lh-fusiform

  Sincerely,



Gonzalo Rojas Costa

On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve
 wrote:
> what is is labled?
>
> On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote:
>>
>> Hi Doug:
>>
>>I use the instructions that you told me... But, why I get the gray
>> colored region (red arrow) ?...
>>
>>Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>>
>>> Message: 15
>>> Date: Mon, 27 May 2013 22:41:41 -0400
>>> From: Douglas Greve 
>>> Subject: Re: [Freesurfer] white matter volume per lobe...
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> you will need to run mri_annotation2label and specify the output to be
>>> an annotation file instead of a segmentation. Then you will have to run
>>> mri_aparc2aseg, specifying your lobes annotation as well as --labelwm
>>> (look in the recon-all.log file for an example of how wmparc.mgz is
>>> created). Then run mri_segstats (you can also get an example from the
>>> recon-all.log file).
>>> doug
>>
>> --
>> Gonzalo Rojas Costa
>> Laboratory for Advanced Medical Image Processing
>> Department of Radiology
>> Clínica las Condes
>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>> Tel: 56-2-2105170
>> Cel: 56-9-97771785
>> www.clc.cl
>
>
> --
> 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/
>
>
>
> 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.
>



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

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Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

You will need to create a new color table. It is currently referencing 
FreeSurferColorLUT.txt. If you load the segmentation as both a 
segmentation and the aux volume, you can see the number associated with 
the color. You will need to create a table similar to FreeSurferColorLUT.txt
doug




On 05/28/2013 01:51 PM, Gonzalo Rojas Costa wrote:
> Hi Doug:
>
>It is labeled as wm-rh-fusiform and wm-lh-fusiform
>
>Sincerely,
>
>
>
> Gonzalo Rojas Costa
>
> On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve
>  wrote:
>> what is is labled?
>>
>> On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote:
>>> Hi Doug:
>>>
>>> I use the instructions that you told me... But, why I get the gray
>>> colored region (red arrow) ?...
>>>
>>> Sincerely,
>>>
>>>
>>> Gonzalo Rojas Costa
>>>
>>>
 Message: 15
 Date: Mon, 27 May 2013 22:41:41 -0400
 From: Douglas Greve 
 Subject: Re: [Freesurfer] white matter volume per lobe...
 To: freesurfer@nmr.mgh.harvard.edu
 Message-ID: <51a41965.6050...@nmr.mgh.harvard.edu>
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 you will need to run mri_annotation2label and specify the output to be
 an annotation file instead of a segmentation. Then you will have to run
 mri_aparc2aseg, specifying your lobes annotation as well as --labelwm
 (look in the recon-all.log file for an example of how wmparc.mgz is
 created). Then run mri_segstats (you can also get an example from the
 recon-all.log file).
 doug
>>> --
>>> Gonzalo Rojas Costa
>>> Laboratory for Advanced Medical Image Processing
>>> Department of Radiology
>>> Clínica las Condes
>>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>>> Tel: 56-2-2105170
>>> Cel: 56-9-97771785
>>> www.clc.cl
>>
>> --
>> 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/
>>
>>
>>
>> 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.
>>
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

[Martijn Steenwijk]

Thanks Doug for your quick reply. But mri_segstats computes the average
value inside the cortical region in the volume, right? That's not wat I
want to have, I want to know the average value of the data in the volume on
the wm/gm surface (i sampled with projfrac = 0).

Any thoughts?



On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve
wrote:

>
> I would use mri_segstats and specify the --annot option
> doug
>
>
> On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
> > Dear all,
> >
> > I've created a custom '.mgh' file containing values on the cortical
> > surface using mri_vol2surf. I would like to compute some statistics on
> > this surface in the aparc-areas computed by freesurfer. Can I then
> > just use  mri_anatomical_stats with option -t specifying the custom
> > mgh file as 'thickness' input? Or does mri_anatomical_stats something
> > more complex than just averaging the values inside each region?
> >
> > Best,
> > Martijn
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

[Douglas N Greve]

It can do both. When you spec --annot, then it does it on the surface 
and you have to pass it surface data (which you already have since you 
ran vol2surf).
doug


On 05/28/2013 02:03 PM, Martijn Steenwijk wrote:
> Thanks Doug for your quick reply. But mri_segstats computes the 
> average value inside the cortical region in the volume, right? That's 
> not wat I want to have, I want to know the average value of the data 
> in the volume on the wm/gm surface (i sampled with projfrac = 0).
>
> Any thoughts?
>
>
>
> On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> I would use mri_segstats and specify the --annot option
> doug
>
>
> On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
> > Dear all,
> >
> > I've created a custom '.mgh' file containing values on the cortical
> > surface using mri_vol2surf. I would like to compute some
> statistics on
> > this surface in the aparc-areas computed by freesurfer. Can I then
> > just use  mri_anatomical_stats with option -t specifying the custom
> > mgh file as 'thickness' input? Or does mri_anatomical_stats
> something
> > more complex than just averaging the values inside each region?
> >
> > Best,
> > Martijn
> >
> >
> > ___
> > 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.
>
>

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

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

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Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

[Martijn Steenwijk]

Sorry, indeed, my reply was too quick. Seems to work, the results are
similar to mri_anatomical_stats.

I'm not sure whether this is relevant; but the sampling seems to be not
equally dense in the different regions. Does mri_segstats somehow cope with
this?

Best,
Martijn

On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk <
martijnsteenw...@gmail.com> wrote:

> Thanks Doug for your quick reply. But mri_segstats computes the average
> value inside the cortical region in the volume, right? That's not wat I
> want to have, I want to know the average value of the data in the volume on
> the wm/gm surface (i sampled with projfrac = 0).
>
> Any thoughts?
>
>
>
> On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> I would use mri_segstats and specify the --annot option
>> doug
>>
>>
>> On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
>> > Dear all,
>> >
>> > I've created a custom '.mgh' file containing values on the cortical
>> > surface using mri_vol2surf. I would like to compute some statistics on
>> > this surface in the aparc-areas computed by freesurfer. Can I then
>> > just use  mri_anatomical_stats with option -t specifying the custom
>> > mgh file as 'thickness' input? Or does mri_anatomical_stats something
>> > more complex than just averaging the values inside each region?
>> >
>> > Best,
>> > Martijn
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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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] mri_anatomical_stats segmentation fault

[Rob Tennyson]

Hi Doug,

It appears that the subject I'm having the PHC issue with has fewer than
163798 vertices - it has 123249 vertices - however, it seems that all of
our subjects have fewer vertices and I do not run into an error with any
other subjects with this label.

Also, I'm able to load the label onto my data in freeview without any
issue. I'm having some problems opening my surfaces with tksurfer on my lab
desktop, though. Should I upload the subjects in question so you can take a
look?

Thanks!
Rob


On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve  wrote:

> Nothing looks like it is wrong with that label. Can you verify that the
> white surface has not been changed since the label was created? Check how
> many vertices the white surface has with mris_info. The PHC label
> references a vertex index as high as 163798. If the white surface does not
> have that many veritices, then that could cause the problem.
> doug
>
>
>
> On 05/28/2013 10:33 AM, Rob Tennyson wrote:
>
>> Hi Doug,
>>
>> Attached are the three labels I'm having an issue with (each with a
>> different subject). These are built from areas that we found functional
>> differences between a healthy control group and a MDD group. I was going to
>> take a look at the anatomical stats to see if there are thickness or volume
>> differences as well.
>>
>> I am also going to review the white surface soon as Bruce suggested.
>>
>>
>> On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> Rob, can you send me your label?
>>
>> doug
>>
>> On 05/27/2013 01:00 PM, Rob Tennyson wrote:
>> > Hi All,
>> >
>> > I'm running "mris_anatomical_stats" with a few manually defined
>> > labels. For a few of my subjects, I am getting the error:
>> > "Segmentation fault" on one of the labels. However, the other
>> manually
>> > defined labels process without any errors on these same subjects.
>> >
>> > For example, I am running "mri_anatomical_stats" on subject 33_bay6
>> > with a manually defined ERC label, a manually defined PHC label,
>> and a
>> > manually defined medial frontal gyrus label. The only label that
>> runs
>> > an error for this subject is the PHC label. This PHC label runs
>> > without any errors on the rest of my subjects.
>> >
>> > Here is what is displayed when running a label that fails:
>> >
>> > "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b
>> > 33_bay6 lh
>> > limiting computations to label lh.PHC_1.label.
>> > reading volume /Volumes/BigRaid/Rob/subjects/**
>> 33_bay6/mri/wm.mgz...
>> > reading input surface
>> > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white...
>> > reading input pial surface
>> > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.pial...
>> > reading input white surface
>> > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white...
>> > Segmentation fault"
>> >
>> > Does anyone know what may be causing the Segmentation fault and what
>> > steps I should take to fix it?
>> >
>> > Thank you for your help!
>> > Rob
>> >
>> >
>> > __**_
>> > 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 > 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 thi

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

[Douglas N Greve]

what do you mean? That the vertices are not uniform? mri_segstats just 
computes the mean over the parcellation without reference to non-uniformity.
doug


On 05/28/2013 02:15 PM, Martijn Steenwijk wrote:
> Sorry, indeed, my reply was too quick. Seems to work, the results are 
> similar to mri_anatomical_stats.
>
> I'm not sure whether this is relevant; but the sampling seems to be 
> not equally dense in the different regions. Does mri_segstats somehow 
> cope with this?
>
> Best,
> Martijn
>
> On Tue, May 28, 2013 at 8:03 PM, Martijn Steenwijk 
> mailto:martijnsteenw...@gmail.com>> wrote:
>
> Thanks Doug for your quick reply. But mri_segstats computes the
> average value inside the cortical region in the volume, right?
> That's not wat I want to have, I want to know the average value of
> the data in the volume on the wm/gm surface (i sampled with
> projfrac = 0).
>
> Any thoughts?
>
>
>
> On Tue, May 28, 2013 at 7:46 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> I would use mri_segstats and specify the --annot option
> doug
>
>
> On 05/28/2013 01:28 PM, Martijn Steenwijk wrote:
> > Dear all,
> >
> > I've created a custom '.mgh' file containing values on the
> cortical
> > surface using mri_vol2surf. I would like to compute some
> statistics on
> > this surface in the aparc-areas computed by freesurfer. Can
> I then
> > just use  mri_anatomical_stats with option -t specifying the
> custom
> > mgh file as 'thickness' input? Or does mri_anatomical_stats
> something
> > more complex than just averaging the values inside each region?
> >
> > Best,
> > Martijn
> >
> >
> > ___
> > 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.
>
>
>

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

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

___
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Re: [Freesurfer] mri_anatomical_stats segmentation fault

[Douglas N Greve]

how did you create the label? If it has more vertices than the subject 
has then something is very wrong. You don't always get segfaults, you 
might just get garbage and never know it.
doug


On 05/28/2013 02:32 PM, Rob Tennyson wrote:
> Hi Doug,
>
> It appears that the subject I'm having the PHC issue with has fewer 
> than 163798 vertices - it has 123249 vertices - however, it seems that 
> all of our subjects have fewer vertices and I do not run into an error 
> with any other subjects with this label.
>
> Also, I'm able to load the label onto my data in freeview without any 
> issue. I'm having some problems opening my surfaces with tksurfer on 
> my lab desktop, though. Should I upload the subjects in question so 
> you can take a look?
>
> Thanks!
> Rob
>
>
> On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Nothing looks like it is wrong with that label. Can you verify
> that the white surface has not been changed since the label was
> created? Check how many vertices the white surface has with
> mris_info. The PHC label references a vertex index as high as
> 163798. If the white surface does not have that many veritices,
> then that could cause the problem.
> doug
>
>
>
> On 05/28/2013 10:33 AM, Rob Tennyson wrote:
>
> Hi Doug,
>
> Attached are the three labels I'm having an issue with (each
> with a different subject). These are built from areas that we
> found functional differences between a healthy control group
> and a MDD group. I was going to take a look at the anatomical
> stats to see if there are thickness or volume differences as well.
>
> I am also going to review the white surface soon as Bruce
> suggested.
>
>
> On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> Rob, can you send me your label?
>
> doug
>
> On 05/27/2013 01:00 PM, Rob Tennyson wrote:
> > Hi All,
> >
> > I'm running "mris_anatomical_stats" with a few manually
> defined
> > labels. For a few of my subjects, I am getting the error:
> > "Segmentation fault" on one of the labels. However, the
> other
> manually
> > defined labels process without any errors on these same
> subjects.
> >
> > For example, I am running "mri_anatomical_stats" on
> subject 33_bay6
> > with a manually defined ERC label, a manually defined
> PHC label,
> and a
> > manually defined medial frontal gyrus label. The only
> label that
> runs
> > an error for this subject is the PHC label. This PHC
> label runs
> > without any errors on the rest of my subjects.
> >
> > Here is what is displayed when running a label that fails:
> >
> > "> mris_anatomical_stats -f PHC.stats.04.txt -l
> lh.PHC_1.label -b
> > 33_bay6 lh
> > limiting computations to label lh.PHC_1.label.
> > reading volume
> /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz...
> > reading input surface
> > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
> > reading input pial surface
> > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial...
> > reading input white surface
> > /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white...
> > Segmentation fault"
> >
> > Does anyone know what may be causing the Segmentation
> fault and what
> > steps I should take to fix it?
> >
> > Thank you for your help!
> > Rob
> >
> >
> > ___
> > 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.nm

Re: [Freesurfer] mri_anatomical_stats segmentation fault

[Rob Tennyson]

The labels are built from areas that showed between-group functional
differences. I am able to view the label on the subject in question in
freeview.

Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps
in the wrong file. I looked at "nvertices" in our "lh.white" file.


On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve
wrote:

> how did you create the label? If it has more vertices than the subject has
> then something is very wrong. You don't always get segfaults, you might
> just get garbage and never know it.
> doug
>
>
>
> On 05/28/2013 02:32 PM, Rob Tennyson wrote:
>
>> Hi Doug,
>>
>> It appears that the subject I'm having the PHC issue with has fewer than
>> 163798 vertices - it has 123249 vertices - however, it seems that all of
>> our subjects have fewer vertices and I do not run into an error with any
>> other subjects with this label.
>>
>> Also, I'm able to load the label onto my data in freeview without any
>> issue. I'm having some problems opening my surfaces with tksurfer on my lab
>> desktop, though. Should I upload the subjects in question so you can take a
>> look?
>>
>> Thanks!
>> Rob
>>
>>
>> On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> Nothing looks like it is wrong with that label. Can you verify
>> that the white surface has not been changed since the label was
>> created? Check how many vertices the white surface has with
>> mris_info. The PHC label references a vertex index as high as
>> 163798. If the white surface does not have that many veritices,
>> then that could cause the problem.
>> doug
>>
>>
>>
>> On 05/28/2013 10:33 AM, Rob Tennyson wrote:
>>
>> Hi Doug,
>>
>> Attached are the three labels I'm having an issue with (each
>> with a different subject). These are built from areas that we
>> found functional differences between a healthy control group
>> and a MDD group. I was going to take a look at the anatomical
>> stats to see if there are thickness or volume differences as well.
>>
>> I am also going to review the white surface soon as Bruce
>> suggested.
>>
>>
>> On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve
>> > > >
>> >
>> >>
>> wrote:
>>
>> Rob, can you send me your label?
>>
>> doug
>>
>> On 05/27/2013 01:00 PM, Rob Tennyson wrote:
>> > Hi All,
>> >
>> > I'm running "mris_anatomical_stats" with a few manually
>> defined
>> > labels. For a few of my subjects, I am getting the error:
>> > "Segmentation fault" on one of the labels. However, the
>> other
>> manually
>> > defined labels process without any errors on these same
>> subjects.
>> >
>> > For example, I am running "mri_anatomical_stats" on
>> subject 33_bay6
>> > with a manually defined ERC label, a manually defined
>> PHC label,
>> and a
>> > manually defined medial frontal gyrus label. The only
>> label that
>> runs
>> > an error for this subject is the PHC label. This PHC
>> label runs
>> > without any errors on the rest of my subjects.
>> >
>> > Here is what is displayed when running a label that fails:
>> >
>> > "> mris_anatomical_stats -f PHC.stats.04.txt -l
>> lh.PHC_1.label -b
>> > 33_bay6 lh
>> > limiting computations to label lh.PHC_1.label.
>> > reading volume
>> /Volumes/BigRaid/Rob/subjects/**33_bay6/mri/wm.mgz...
>> > reading input surface
>> > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white...
>> > reading input pial surface
>> > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.pial...
>> > reading input white surface
>> > /Volumes/BigRaid/Rob/subjects/**33_bay6/surf/lh.white...
>> > Segmentation fault"
>> >
>> > Does anyone know what may be causing the Segmentation
>> fault and what
>> > steps I should take to fix it?
>> >
>> > Thank you for your help!
>> > Rob
>> >
>> >
>> > __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> 
>> > >
>> 
>> >
>> 
>> > >>
>>
>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> fre

Re: [Freesurfer] mri_anatomical_stats segmentation fault

[Douglas N Greve]

The label that you sent applies to fsaverage. If you want to use it on a 
different subject, you should map it to that subject with mri_label2label
doug



On 05/28/2013 03:00 PM, Rob Tennyson wrote:
> The labels are built from areas that showed between-group functional 
> differences. I am able to view the label on the subject in question in 
> freeview.
>
> Maybe I'm looking at the wrong place in the output of mris_info? Or 
> perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file.
>
>
> On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> how did you create the label? If it has more vertices than the
> subject has then something is very wrong. You don't always get
> segfaults, you might just get garbage and never know it.
> doug
>
>
>
> On 05/28/2013 02:32 PM, Rob Tennyson wrote:
>
> Hi Doug,
>
> It appears that the subject I'm having the PHC issue with has
> fewer than 163798 vertices - it has 123249 vertices - however,
> it seems that all of our subjects have fewer vertices and I do
> not run into an error with any other subjects with this label.
>
> Also, I'm able to load the label onto my data in freeview
> without any issue. I'm having some problems opening my
> surfaces with tksurfer on my lab desktop, though. Should I
> upload the subjects in question so you can take a look?
>
> Thanks!
> Rob
>
>
> On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> Nothing looks like it is wrong with that label. Can you verify
> that the white surface has not been changed since the
> label was
> created? Check how many vertices the white surface has with
> mris_info. The PHC label references a vertex index as high as
> 163798. If the white surface does not have that many
> veritices,
> then that could cause the problem.
> doug
>
>
>
> On 05/28/2013 10:33 AM, Rob Tennyson wrote:
>
> Hi Doug,
>
> Attached are the three labels I'm having an issue with
> (each
> with a different subject). These are built from areas
> that we
> found functional differences between a healthy control
> group
> and a MDD group. I was going to take a look at the
> anatomical
> stats to see if there are thickness or volume
> differences as well.
>
> I am also going to review the white surface soon as Bruce
> suggested.
>
>
> On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve
>  
>  >
>  
>
>  
> Rob, can you send me your label?
>
> doug
>
> On 05/27/2013 01:00 PM, Rob Tennyson wrote:
> > Hi All,
> >
> > I'm running "mris_anatomical_stats" with a few
> manually
> defined
> > labels. For a few of my subjects, I am getting
> the error:
> > "Segmentation fault" on one of the labels.
> However, the
> other
> manually
> > defined labels process without any errors on
> these same
> subjects.
> >
> > For example, I am running "mri_anatomical_stats" on
> subject 33_bay6
> > with a manually defined ERC label, a manually
> defined
> PHC label,
> and a
> > manually defined medial frontal gyrus label. The
> only
> label that
> runs
> > an error for this subject is the PHC label. This PHC
> label runs
> > without any errors on the rest of my subjects.
> >
> > Here is what is displayed when running a label
> that fails:
> >
> > "> mris_anatomical_stats -f PHC.stats.04.txt -l
> lh.PHC_1.label -b
> > 33_bay6 lh
> > limiting computations to label lh.PHC_1.label.
> > reading volume
> /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mg

Re: [Freesurfer] mri_anatomical_stats segmentation fault

[Rob Tennyson]

That explains a lot about my problem subjects.

Just to confirm, I should use mri_label2label with fsaverage as the source
subject and the subject in question as the target? Having this run for all
of my subjects will then allow me to use mris_anatomical_stats for each
subject.

Thanks for the help!


On Tue, May 28, 2013 at 2:06 PM, Douglas N Greve
wrote:

> The label that you sent applies to fsaverage. If you want to use it on a
> different subject, you should map it to that subject with mri_label2label
> doug
>
>
>
>
> On 05/28/2013 03:00 PM, Rob Tennyson wrote:
>
>> The labels are built from areas that showed between-group functional
>> differences. I am able to view the label on the subject in question in
>> freeview.
>>
>> Maybe I'm looking at the wrong place in the output of mris_info? Or
>> perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file.
>>
>>
>> On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> how did you create the label? If it has more vertices than the
>> subject has then something is very wrong. You don't always get
>> segfaults, you might just get garbage and never know it.
>> doug
>>
>>
>>
>> On 05/28/2013 02:32 PM, Rob Tennyson wrote:
>>
>> Hi Doug,
>>
>> It appears that the subject I'm having the PHC issue with has
>> fewer than 163798 vertices - it has 123249 vertices - however,
>> it seems that all of our subjects have fewer vertices and I do
>> not run into an error with any other subjects with this label.
>>
>> Also, I'm able to load the label onto my data in freeview
>> without any issue. I'm having some problems opening my
>> surfaces with tksurfer on my lab desktop, though. Should I
>> upload the subjects in question so you can take a look?
>>
>> Thanks!
>> Rob
>>
>>
>> On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve
>> > > >
>>  > >>
>> wrote:
>>
>> Nothing looks like it is wrong with that label. Can you verify
>> that the white surface has not been changed since the
>> label was
>> created? Check how many vertices the white surface has with
>> mris_info. The PHC label references a vertex index as high as
>> 163798. If the white surface does not have that many
>> veritices,
>> then that could cause the problem.
>> doug
>>
>>
>>
>> On 05/28/2013 10:33 AM, Rob Tennyson wrote:
>>
>> Hi Doug,
>>
>> Attached are the three labels I'm having an issue with
>> (each
>> with a different subject). These are built from areas
>> that we
>> found functional differences between a healthy control
>> group
>> and a MDD group. I was going to take a look at the
>> anatomical
>> stats to see if there are thickness or volume
>> differences as well.
>>
>> I am also going to review the white surface soon as Bruce
>> suggested.
>>
>>
>> On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve
>> > 
>> > >
>> 
>> > 
>>
>> 
>> > > wrote:
>>
>> Rob, can you send me your label?
>>
>> doug
>>
>> On 05/27/2013 01:00 PM, Rob Tennyson wrote:
>> > Hi All,
>> >
>> > I'm running "mris_anatomical_stats" with a few
>> manually
>> defined
>> > labels. For a few of my subjects, I am getting
>> the error:
>> > "Segmentation fault" on one of the labels.
>> However, the
>> other
>> manually
>> > defined labels process without any errors on
>> these same
>> subjects.
>> >
>> > For example, I am running "mri_anatomical_stats" on
>> subject 33_bay6
>> > with a manually defined ERC label, a manually
>> defined
>> PHC label,
>> and a
>> > manually defined medial frontal gyrus label. The
>> only
>> label that
>> runs
>> > an error for this subject is the PHC labe

Re: [Freesurfer] mri_anatomical_stats segmentation fault

[Douglas N Greve]

yes
On 05/28/2013 03:15 PM, Rob Tennyson wrote:
> That explains a lot about my problem subjects.
>
> Just to confirm, I should use mri_label2label with fsaverage as the 
> source subject and the subject in question as the target? Having this 
> run for all of my subjects will then allow me to use 
> mris_anatomical_stats for each subject.
>
> Thanks for the help!
>
>
> On Tue, May 28, 2013 at 2:06 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> The label that you sent applies to fsaverage. If you want to use
> it on a different subject, you should map it to that subject with
> mri_label2label
> doug
>
>
>
>
> On 05/28/2013 03:00 PM, Rob Tennyson wrote:
>
> The labels are built from areas that showed between-group
> functional differences. I am able to view the label on the
> subject in question in freeview.
>
> Maybe I'm looking at the wrong place in the output of
> mris_info? Or perhaps in the wrong file. I looked at
> "nvertices" in our "lh.white" file.
>
>
> On Tue, May 28, 2013 at 1:52 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> how did you create the label? If it has more vertices than the
> subject has then something is very wrong. You don't always get
> segfaults, you might just get garbage and never know it.
> doug
>
>
>
> On 05/28/2013 02:32 PM, Rob Tennyson wrote:
>
> Hi Doug,
>
> It appears that the subject I'm having the PHC issue
> with has
> fewer than 163798 vertices - it has 123249 vertices -
> however,
> it seems that all of our subjects have fewer vertices
> and I do
> not run into an error with any other subjects with
> this label.
>
> Also, I'm able to load the label onto my data in freeview
> without any issue. I'm having some problems opening my
> surfaces with tksurfer on my lab desktop, though. Should I
> upload the subjects in question so you can take a look?
>
> Thanks!
> Rob
>
>
> On Tue, May 28, 2013 at 10:06 AM, Douglas N Greve
>  
>  >
>  
>  
> Nothing looks like it is wrong with that label.
> Can you verify
> that the white surface has not been changed since the
> label was
> created? Check how many vertices the white surface
> has with
> mris_info. The PHC label references a vertex index
> as high as
> 163798. If the white surface does not have that many
> veritices,
> then that could cause the problem.
> doug
>
>
>
> On 05/28/2013 10:33 AM, Rob Tennyson wrote:
>
> Hi Doug,
>
> Attached are the three labels I'm having an
> issue with
> (each
> with a different subject). These are built
> from areas
> that we
> found functional differences between a healthy
> control
> group
> and a MDD group. I was going to take a look at the
> anatomical
> stats to see if there are thickness or volume
> differences as well.
>
> I am also going to review the white surface
> soon as Bruce
> suggested.
>
>
> On Tue, May 28, 2013 at 9:26 AM, Douglas N Greve
>  
>  >
>  
>  >>
>  
>  >
>
>  
>   wrote:
>
> 

Re: [Freesurfer] LME toolbox - univariate

[Martin Reuter]

Hi Yolanda,

since you have the intercept you don't need both group1 and group2 (as 
one is  1 - the other), so drop beta 5 and 6 terms.
If you want to test if the slope is different between the groups differ 
just look at beta4 which is checking if slope1-slope2 different from 
zero. If it is negative slope2 is larger, if positive slope1 is larger. 
Note that if your slopes are negative, e.g. atrophy, then larger means 
closer to zero = less atrophy.


Best, Martin

On 05/28/2013 11:57 AM, Yolanda Vives wrote:

Dear FreeSurfer experts,

I am trying to use the LME toolbox to analyse the hippocampal change 
over time in a group and also among 2 groups (2 scans per subject).


When I estimate the parameters with lme_fit_FS I become a warning 
saying that the matrix is singular and my results are NaN. I guess 
that my design matrix X is not correct, can you please help me?


I have followed the example from the wiki. My model for the two groups 
study is the following:


Y_ij = ß_1 + ß_2 *t_ij +ß_3 *Group1 + ß_4 *Group1 *t_ij + ß_5 *Group2 
+ ß_6 *Group2 *t_ij + ß_7 *Gender_i + ß_8 *Age_i + ß_9 *ICV_i + b_1i + 
b_2i *t_ij + e_ij


1) intercept (all ones)

2) time (t_ij ) . Here I have 0s for the first scan of each subject 
and a number in years for the second scans. Is it correct?


3) one for Group1 and zero otherwise

4) colum 3) .* time

5) one for Group2 and zero otherwise

6) colum 5) .* time

7) Gender

8) Age of the subject at each scan moment.

9) ICV (converted to liters).

Thank you in advance,
Yolanda


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--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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[Freesurfer] recon-all error: v5.0.0 - dataset 1

[Sudhin A. Shah]

BEST FITNESS (M) is 984.24263
 mri =0.000   curv = 4.318 unmri = -1001.515
 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64  )
 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
  63 patches have been generated - 38 self-intersected
  max face = 36973(40653) - loop = 46 (73)  - ntries = [27,14799]

ERROR: _FindFacePath: could not find path!
Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 
5 19:39:49 UTC 2012 x86_64 GNU/Linux

recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013


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[Freesurfer] recon-all error: v5.0.0 - dataset 3

[Sudhin A. Shah]

CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal vector of length zero at vertex 88778 with 0 faces
vertex 88778 has 0 face
No such file or directory
Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 
5 19:39:49 UTC 2012 x86_64 GNU/Linux

recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013

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[Freesurfer] recon-all error: v5.0.0 - dataset 2

[Sudhin A. Shah]

===
*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.

Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 
5 19:39:49 UTC 2012 x86_64 GNU/Linux

recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013
==

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[Freesurfer] recon-all errors: v5.0.0; dataset 4

[Sudhin A. Shah]

CORRECTING DEFECT 1 (vertices=33, convex hull=57)
After retessellation of defect 1, euler #=-41 (88676,260208,171491) : 
difference with theory (-61) = -20

CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal vector of length zero at vertex 88778 with 0 faces
vertex 88778 has 0 face
No such file or directory
Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 
5 19:39:49 UTC 2012 x86_64 GNU/Linux

recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49 EDT 2013

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Re: [Freesurfer] recon-all error: v5.0.0 - dataset 1

[Bruce Fischl]

the new topo fixer will correct this problem
Bruce
On Tue, 28 May 2013, Sudhin A. 
Shah wrote:





BEST FITNESS (M) is 984.24263
 mri =0.000   curv = 4.318 unmri = -1001.515
 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64  )
 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
  63 patches have been generated - 38 self-intersected
  max face = 36973(40653) - loop = 46 (73)  - ntries = [27,14799]

ERROR: _FindFacePath: could not find path!
Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 
5 19:39:49 UTC 2012 x86_64
GNU/Linux

recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013



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Re: [Freesurfer] recon-all error: v5.0.0 - dataset 2

[Bruce Fischl]

Hi Sudhin

you need to track down why this happened. First thing to look at is the 
tal xform
Bruce
On Tue, 28 May 2013, Sudhin A. Shah wrote:

> 
> 
> ===
> *WATERSHED**
> Sorting...
> mri_watershed Error:
> Problem in the COG calculation:
> T1.mgz may not contain properly normalized white-matter.
> Confirm that T1.mgz has enough white-matter voxels of value 110.
> If white-matter contains few if any voxels of value 110,
> try adding wm control-points to nu.mgz, and re-run recon-all.
> 
> Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon 
> Mar 5 19:39:49 UTC 2012 x86_64
> GNU/Linux
> 
> recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013
> ==
> 
> 
>
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[Freesurfer] hipposubfields and data

[Joshua Lee]

I have read that the hippo-subfield algorithm uses the aseg for
initialization, and then uses the original MRI data. By original, does that
mean it up-samples the conformed 1mm data to .5mm, or does that mean it
takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and
upsamples it to .5mm?

Josh
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Re: [Freesurfer] hipposubfields and data

[Juan Eugenio Iglesias]

Hi Josh,
as of now, it uses nu.mgz, which is conformed and bias field corrected
with N3. 
Koen, do you think we should add a flag to change this? The algorithm is
pretty resolution-independent, and could certainly benefit from
higher-res data.
Cheers,
/Eugenio

On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote:
> I have read that the hippo-subfield algorithm uses the aseg for
> initialization, and then uses the original MRI data. By original, does
> that mean it up-samples the conformed 1mm data to .5mm, or does that
> mean it takes the original original input (i.e. my 0.7 mm isotropic
> MPRAGE) and upsamples it to .5mm?
> 
> Josh
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-- 
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http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.



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Re: [Freesurfer] hipposubfields and data

[Joshua Lee]

I think the resolution is important. The CA1 subfield is only about 2-2.5
mm thick after all.

If this is a feature request thread now, let me add that it would be nice
if the actual training algorithm was integrated into Freesurfer. There is a
lot of disagreement about the most appropriate subfield boundaries, and the
ability to make custom training sets would be helpful.

Right now there is little guidance on what kind of data-sets are
appropriate to use with this algorithm. I am concerned that users are
trying to segment subfields with older data-sets that probably aren't
appropriate (e.g. 1.5 Tesla or 1.5 mm isotropic data).


Josh


On Tue, May 28, 2013 at 1:44 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

> Hi Josh,
> as of now, it uses nu.mgz, which is conformed and bias field corrected
> with N3.
> Koen, do you think we should add a flag to change this? The algorithm is
> pretty resolution-independent, and could certainly benefit from
> higher-res data.
> Cheers,
> /Eugenio
>
> On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote:
> > I have read that the hippo-subfield algorithm uses the aseg for
> > initialization, and then uses the original MRI data. By original, does
> > that mean it up-samples the conformed 1mm data to .5mm, or does that
> > mean it takes the original original input (i.e. my 0.7 mm isotropic
> > MPRAGE) and upsamples it to .5mm?
> >
> > Josh
> > ___
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>
> --
> Juan Eugenio Iglesias, PhD
> http://www.jeiglesias.com
> igles...@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
>
>
>
>
>
> 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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Re: [Freesurfer] recon-all error: v5.0.0 - dataset 1

[Sudhin A. Shah]

Hi! Can you please send this to me?

On May 28, 2013, at 4:24 PM, Bruce Fischl wrote:

> the new topo fixer will correct this problem
> Bruce
> On Tue, 28 May 2013, Sudhin A. Shah wrote:
> 
>> BEST FITNESS (M) is 984.24263
>>  mri =0.000   curv = 4.318 unmri = -1001.515
>>  ( f=0.00 , v=0.00 , c=4.32 , q= 8.64  )
>>  ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
>>   63 patches have been generated - 38 self-intersected
>>   max face = 36973(40653) - loop = 46 (73)  - ntries = [27,14799]
>> ERROR: _FindFacePath: could not find path!
>> Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon 
>> Mar 5 19:39:49 UTC 2012 x86_64
>> GNU/Linux
>> recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013
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[Freesurfer] SUMA and FSFAST

[Joseph Dien]

I was wondering if someone could give me a summary as to how SUMA and FSFAST 
differ?  In other words, user interface aside, what would be reasons to use one 
or the other?

Joe




Joseph Dien,
Senior Research Scientist
University of Maryland 

E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//











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Re: [Freesurfer] Subcortical Structures not included in GM surfaces

[Bruce Fischl]

It doesn't need fixing. Those regions aren't part of cortex and the surfaces 
are arbitrary there (but excluded from thickness calculations)



On May 28, 2013, at 7:39 PM, Jonathan Holt  wrote:

> Is this normal, attached slide shows a rather common occurrence for me. Half 
> of the amygdala (blue) is included in pial surface, while the other is not. 
> How should I go about fixing, the local WM is perfectly fine so I'm not sure 
> where to start.
> 
> 
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[Freesurfer] Fwd: Re: mris_resample: Command not found.

[zkaufman]

Daniel, Stefano, Others,

A patch is now available for the "mris_resample : Command not found" 
error you encountered.

Simply download the file from the following link and place it in your
$FREESURFER_HOME/bin directory:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample

Feel free to contact me if you have any additional questions/issues.

-Zeke


 Original Message 
Subject: Re: [Freesurfer] mris_resample: Command not found.
Date: Tue, 28 May 2013 11:41:21 -0400
From: Z K 
To: Barron, Daniel S 
CC: freesurfer@nmr.mgh.harvard.edu ,
 Lilla Zollei 

Hello Daniel,

This is a confirmed issue with the 64bit Mac build. A patch to fix the
issue will be available shortly (~hours). I will email the list and you
personally once it is available. Sorry for the inconvenience.

-Zeke

On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
> Hi Lilla,
> I'm using OSX 10.8.3
> Thanks,
> Daniel
> 
> From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu]
> Sent: Tuesday, May 28, 2013 10:04 AM
> To: Barron, Daniel S
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: mris_resample: Command not found.
> Hi Daniel,
> What operating system are you using?
> Lilla
> On Tue, 28 May 2013, Barron, Daniel S wrote:
>> Hello,
>> I am trying to perform an inter-subject registration using
mri_cvs_register on version 5.3.
>> When I ran mri_cvs_check, my feedback was I needed to find
"mri_cvs_register.settings.txt" but I didn't worry about this per
Lilla's post:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html
>> mri_cvs_register kicks off well, but eventually it ends with:
>> "mris_resample: Command not found."
>> I go into my $FREESURFER_HOME/bin directory and note that mris_resample
is truly not there.  Did I not install 5.3 properly?
>> I have attached a log file in case this helps.
>> Cheers,
>> Daniel
> 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] mris_resample: Command not found.

[Barron, Daniel S]

Thanks for the path, Zeke. 

Because it didn't download as an executable file to my computer, I used "chmod 
+x ~/mris_resample" (FYI for others?)

It looks to be running normally. Will report back when finished!

Thanks again,
Daniel


On May 28, 2013, at 11:25 PM, 
 wrote:

> Daniel, Stefano, Others,
> 
> A patch is now available for the "mris_resample : Command not found" 
> error you encountered.
> 
> Simply download the file from the following link and place it in your
> $FREESURFER_HOME/bin directory:
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
> 
> Feel free to contact me if you have any additional questions/issues.
> 
> -Zeke
> 
> 
>  Original Message 
> Subject: Re: [Freesurfer] mris_resample: Command not found.
> Date: Tue, 28 May 2013 11:41:21 -0400
> From: Z K 
> To: Barron, Daniel S 
> CC: freesurfer@nmr.mgh.harvard.edu ,
> Lilla Zollei 
> 
> Hello Daniel,
> 
> This is a confirmed issue with the 64bit Mac build. A patch to fix the
> issue will be available shortly (~hours). I will email the list and you
> personally once it is available. Sorry for the inconvenience.
> 
> -Zeke
> 
> On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
>> Hi Lilla,
>> I'm using OSX 10.8.3
>> Thanks,
>> Daniel
>> 
>> From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, May 28, 2013 10:04 AM
>> To: Barron, Daniel S
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: mris_resample: Command not found.
>> Hi Daniel,
>> What operating system are you using?
>> Lilla
>> On Tue, 28 May 2013, Barron, Daniel S wrote:
>>> Hello,
>>> I am trying to perform an inter-subject registration using
> mri_cvs_register on version 5.3.
>>> When I ran mri_cvs_check, my feedback was I needed to find
> "mri_cvs_register.settings.txt" but I didn't worry about this per
> Lilla's post:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html
>>> mri_cvs_register kicks off well, but eventually it ends with:
>>> "mris_resample: Command not found."
>>> I go into my $FREESURFER_HOME/bin directory and note that mris_resample
> is truly not there.  Did I not install 5.3 properly?
>>> I have attached a log file in case this helps.
>>> Cheers,
>>> Daniel
>> 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
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> 
> 
> 
> 
> 
> 
> 
> 



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[Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

I need to extract the beta weights from a cluster identified with FS-Fast in 
order to compute percentage signal change.  

1) I see a file called beta.nii.gz that appears to have the beta weight 
information.  It has a four dimensional structure and the fourth dimension 
appears to be the beta weights.  Is there an index somewhere as to which beta 
weight is which?  Or if not, how are they organized?

2) In order to extract the cluster, it looks like I would use mri_label2vol to 
convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged 
with the number of the corresponding cluster.

I could then use that to generate masks to extract the information I need for 
each cluster from beta.nii.gz.

Is that correct?

3) The final information that I would need is the canonical hrf shape generated 
by FSFAST for a single event.  I guess I could generate that by setting up a 
dummy analysis run with a single event of the desired duration and then look in 
the X variable in the resulting X.mat file?

Sorry for all the questions!

Joe






Joseph Dien,
Senior Research Scientist
University of Maryland 

E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//











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