Re: [Freesurfer] Cortical thickness

[Joshua deSouza]

Hello Doug,

Each individuals subject data has already been smoothed by 5 10 15 20 and
25 through the qache function during the initial processing.

I'm a little confused now. I thought that the mri_preproc would use the
non-smoothed values of the subjects and create an mgh file. After which I
smooth the mgh file and then use mri_glmfit to analyse it according to the
contrasts.

If the above is not the case and the subject data has already been
smoothed, then what should I do if I wish my final mgh file to have a
smoothing value of 15 before doing a glmfit on it?

Thank you,

Joshua


On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza
wrote:

> Hello Doug,
>
> Each individuals subject data has already been smoothed by 5 10 15 20 and
> 25 through the qache function during the initial processing.
>
> I'm a little confused now. I thought that the mri_preproc would use the
> non-smoothed values of the subjects and create an mgh file. After which I
> smooth the mgh file and then use mri_glmfit to analyse it according to the
> contrasts.
>
> If the above is not the case and the subject data has already been
> smoothed, then what should I do if I wish my final mgh file to have a
> smoothing value of 15 before doing a glmfit on it?
>
> Thank you,
>
> Joshua
>
> On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve 
> wrote:
>
>>
>> Hi Joshua, when you add --fwhm 15 to the command line you are instructing
>> mri_glmfit to smooth by 15mm. Is this what you want?  Or is the data
>> already smoothed?
>> doug
>>
>>
>>
>> On 6/3/13 12:26 AM, Joshua deSouza wrote:
>>
>> Hi Doug,
>>
>> The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C
>> t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir
>>
>> I am doing a whole hemisphere analysis and am measuring cortical
>> thickness. I do not have my own mask but I have doubts about the mask that
>> has been produced because from previous studies, there has been significant
>> thinning in the area around the hippocampus and parts of it are being left
>> out in the mask, such as the para-hippocampal region.
>>
>> Regards
>>
>> Joshua
>>
>> On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve > > wrote:
>>
>>>
>>> The residual FWHM is measured from the data itself. You apply a certain
>>> amount of smoothing, but there is already some smoothness to the data, so
>>> the final fwhm is a combination of what is already there and what you
>>> apply. A fwhm of 47 is huge and may indicate that something is wrong. What
>>> is the input? cortical thickness? Are you using your own mask or is this a
>>> whole hemisphere analysis?
>>>
>>> doug
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 6/2/13 10:29 PM, Joshua deSouza wrote:
>>>
>>> Hello Doug,
>>>
>>> Thank you for your quick replies to my queries. Really appreciate it.
>>>
>>> I have found the files containing the cortical thickness values. Thank
>>> you. I assume that the order in which they follow are based on the fsgd
>>> file and the cluster annotation numbers.
>>>
>>> I was just slightly confused about the residual fwhm. I have already
>>> done a smoothing of 15 on the file and have recieved a residual value of
>>> 47, which I assume is extremely large. Since I'm finding out values for the
>>> entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of
>>> 47. Could you please tell me what the residual values mean?  What do you
>>> recommend I do? Is there anything I can read up on to find out more about
>>> this? (Please pardon my questions if they seem a little trivial)
>>>
>>> Thank you
>>>
>>> Joshua
>>>
>>> On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>

 This file is always created by mri_glmfit-sim. It might be named
 something different depending on your parameters (should always end in
 y.ocn.dat)
 doug


 On 6/2/13 3:57 AM, Joshua deSouza wrote:

 Hi Doug,

  This file that your saying, will be created after glmfit-sim is done
 using the cache function and a threshold of 1.3 and absolute ,with y being
 the fsgd file? Am I understanding this correctly?

  Thank you

  Joshua

 On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve <
 gr...@nmr.mgh.harvard.edu> wrote:

> There should be a file called something like cache.th13.abs.y.ocn.dat.
> This will have a column for each cluster and a row for each subject.
> The
> value in the row will be the input for each subject.
> doug
>
> On 05/30/2013 11:21 PM, Joshua deSouza wrote:
> > Hello everyone,
> >
> > Please pardon my rather simple question
> >
> > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf
> > with a few others after the analysis.As I know, I do not have to
> > create ROIs in order to do this. I also understand that doing a
> > multiple comparison analysis just compares the regions of importance
> > and evaluates them giving the most resilien

Re: [Freesurfer] mris_preproc --qdec-long problem

[Martin Reuter]

Hi Chris,

still the same (kind of) problem. For some reason you are getting an 
empty line in the qdec table so it expands the name to
".long." .  Open your long.qdec.table.dat in an editor (e.g. nedit or 
gedit), maybe try to copy it into a new editor window, safe it and hope 
the editor fixes the problem.

Also try
cat ./qdec/long.qdec.table.dat
to see what it prints, there should be no empty lines.

You can also use hexdump -cb ./qdec/long.qdec.table.dat
to take a look at the files content, there should be single \n at the 
end of each line.


Best, Martin

On 06/04/2013 01:41 PM, Christopher McCarthy wrote:

Dr. Reuter,

Thanks for your help, it got me through the error I was having.  On to 
the next one:


When I enter the command:

mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage 
--hemi lh --meas thickness --out lh.thickness.mgh


it spits out the following two lines before quitting:

nsubjects = 45
ERROR: cannot find /media/freesurfer/.long.

Any idea what I'm missing?

Thanks for your help and patience,

Chris


On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>> wrote:


Hi Chris,

this is a good question for the list (cc'ed), others may or will
have the same problem.

The problem is with your table file, specifically the new line
character. DOS uses \r\n , Mac \r and Linux \n.
Your text file uses \r, so it probably was created on a mac.

The problem is that the "cat" command (at least in linux) does not
work on your file:
cat long.qdec.table.dat is empty

You can convert the \r to \n (linux format):
 tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat

and then should be able to run the preproc command.

People with DOS formats should not run the above "tr' command as
they will end up with 2 newlines instead of 1. Maybe DOS txt files
work with 'cat' directly (so there is no need)? If anyone on the
list knows a good way of cat and awk a file independently of the
new line (and working on all OS), let me know. This is the command
I use:

cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#")
printf("%s.long.%s\n", $1, $2)}'

to generate the subjects id's from the table's first two columns.

Best, Martin



On 06/03/2013 03:45 PM, Christopher McCarthy wrote:

Dr. Reuter,

We corresponded in the past about QDEC, and you gave me great
help.  The lab I work for is now moving towards using the
Longitudinal Mixed Effects Model.  When I go to run the command:

mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target
study_average --hemi lh --meas thickness --out lh.thickness.mgh

I get the error: 'ERROR: no subjects specified.'  I am
attaching my long.qdec.table.dat, which works fine when loaded
by QDEC.  Do you have any idea of why I am getting this error?

Thanks,

Chris McCarthy


-- 
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



The information in this e-mail is intended only for the person to
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the e-mail
contains patient information, please contact the Partners
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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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3

[Mehul Sampat]

Oh, I see it would prevent us from getting the aseg.stats file.
That's not good; we want the whole enchilada :-)

Never mind; will follow your previous suggestion and run recon-all all the
way through;
Thanks Doug;

Mehul




On Tue, Jun 4, 2013 at 11:41 AM, Douglas N Greve
wrote:

>
> It would stop the error but still prevent you from getting the stats file.
> If you don't need the stats file, you can add -nosegstats to the cmd line
> as the last option.
> doug
>
>
>
> On 06/04/2013 02:32 PM, Mehul Sampat wrote:
>
>> Hi Doug,
>>
>> Thanks; Will do so.
>>
>> Also I forgot to mention one thing in the previous email:
>>
>> for case -autorecon3, also there is:
>> set DoSegStats   = 1; (in recon-all script in 5.3 this is line 5526)
>>
>> would it help, if  "set DoSegStats   = 1" was used only in
>> -autorecon3 and not in the
>> -autorecon2 or -autorecon2-cp ? or would this break other stuff.
>>
>> Mehul
>>
>>
>>
>>
>>
>> On Tue, Jun 4, 2013 at 11:24 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> this is a bug in mri_segstats. For now, you will need to run
>> recon-all to the end to generate the ribbon.mgz file
>> doug
>>
>> On 06/04/2013 02:12 PM, Mehul Sampat wrote:
>>
>> Hi Doug,
>> Yes, we see the same error as in msg28047.html; here is the
>> line from my recon-all.log:
>>
>> mghRead(/mnt/horizon/stage/**HLC//004_151_3106223
>> /WBS/Baseline/**Freesurfer/mri/ribbon.mgz, -1):
>>
>> could not open file
>>
>> In msg28047.html, Milkos suggested that the issue could be the
>> following line in recon-all
>> "  set DoSegStats = 1"
>>
>> (in recon-all script in 5.2 this is line 5225; under the case
>> "-autorecon2" )
>> (in recon-all script in 5.3 this is line 5401; under the case
>> "-autorecon2" )
>>
>> I think he is right; first i was confused why this issue was
>> not seen with -autrecon2-cp
>>
>> because there is "  set DoSegStats   = 1"  for
>> -autrecon2-cp too;
>> (in recon-all script in 5.3 this is line 5480; under the case
>> "-autorecon2-cp")
>>
>> But normally we run -autorecon3 or -all before running
>> -autorecon2-cp; so in this case
>> the ribbon exists and the error does not show up with
>>  -autorecon2-cp (if -all or -autorecon3 is run before).
>>
>> Mehul
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Jun 4, 2013 at 10:49 AM, Douglas N Greve
>> > > >
>> >
>> >>
>> wrote:
>>
>> The error in  msg28047.html is that there was no
>> ribbon.mgz. Is
>> that the
>> error you are receiving?
>>> freesur...@nmr.mgh.harvard.**edu/msg28047.html
>> >
>> On 06/04/2013 01:45 PM, Mehul Sampat wrote:
>> > Hi Zeke,
>> > Thanks for looking into this; had a quick followup item
>> to report.
>> > So for the same subject  "recon-all -all" runs through
>> smoothly;
>> > (it was only recon-all -autorecon1 -autorecon2 that
>> generated
>> the error)
>> >
>> > I had not seen the error before since in the past, my
>> workflow
>> was as
>> > follows:
>> >
>> > 1. run recon-all with -all
>> > 2. add control points if required
>> > 3. run recon-all with -autorecon2-cp and autorecon3
>> >
>> > This ran through without any errors;
>> >
>> > Now to save some processing time, the modified workflow is:
>> > 1. run recon-all with -autorecon1 -autorecon2
>> > 2. add control points if required
>> > 3. run recon-all with -autorecon2-cp and autorecon3
>> > (It was step 1 in this modified workflow that generated
>> the issue)
>> >
>> > Mehul
>> > ps: the recon-all.log file from the error reported
>> earlier is
>> attached
>> > for reference (i sent it to you but forgot to send it to
>> the mailing
>> > list earlier)
>> >
>> >
>> >
>> >
>> > On Thu, May 30, 2013 at 8:31 AM, Z K
>> > > >
>> > > >>
>> > 
>> > > >
>>
>> 
>> 

Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3

[Mehul Sampat]

Hi Doug,

Thanks; Will do so.

Also I forgot to mention one thing in the previous email:

for case -autorecon3, also there is:
set DoSegStats   = 1; (in recon-all script in 5.3 this is line 5526)

would it help, if  "set DoSegStats   = 1" was used only in -autorecon3
and not in the
-autorecon2 or -autorecon2-cp ? or would this break other stuff.

Mehul





On Tue, Jun 4, 2013 at 11:24 AM, Douglas N Greve
wrote:

> this is a bug in mri_segstats. For now, you will need to run recon-all to
> the end to generate the ribbon.mgz file
> doug
>
> On 06/04/2013 02:12 PM, Mehul Sampat wrote:
>
>> Hi Doug,
>> Yes, we see the same error as in msg28047.html; here is the line from my
>> recon-all.log:
>>
>> mghRead(/mnt/horizon/stage/**HLC//004_151_3106223/WBS/**
>> Baseline/Freesurfer/mri/**ribbon.mgz, -1): could not open file
>>
>> In msg28047.html, Milkos suggested that the issue could be the following
>> line in recon-all
>> "  set DoSegStats = 1"
>>
>> (in recon-all script in 5.2 this is line 5225; under the case
>> "-autorecon2" )
>> (in recon-all script in 5.3 this is line 5401; under the case
>> "-autorecon2" )
>>
>> I think he is right; first i was confused why this issue was not seen
>> with -autrecon2-cp
>>
>> because there is "  set DoSegStats   = 1"  for -autrecon2-cp too;
>> (in recon-all script in 5.3 this is line 5480; under the case
>> "-autorecon2-cp")
>>
>> But normally we run -autorecon3 or -all before running -autorecon2-cp; so
>> in this case
>> the ribbon exists and the error does not show up with  -autorecon2-cp (if
>> -all or -autorecon3 is run before).
>>
>> Mehul
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Jun 4, 2013 at 10:49 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> The error in  msg28047.html is that there was no ribbon.mgz. Is
>> that the
>> error you are receiving?
>> > edu/msg28047.html
>> >
>> On 06/04/2013 01:45 PM, Mehul Sampat wrote:
>> > Hi Zeke,
>> > Thanks for looking into this; had a quick followup item to report.
>> > So for the same subject  "recon-all -all" runs through smoothly;
>> > (it was only recon-all -autorecon1 -autorecon2 that generated
>> the error)
>> >
>> > I had not seen the error before since in the past, my workflow
>> was as
>> > follows:
>> >
>> > 1. run recon-all with -all
>> > 2. add control points if required
>> > 3. run recon-all with -autorecon2-cp and autorecon3
>> >
>> > This ran through without any errors;
>> >
>> > Now to save some processing time, the modified workflow is:
>> > 1. run recon-all with -autorecon1 -autorecon2
>> > 2. add control points if required
>> > 3. run recon-all with -autorecon2-cp and autorecon3
>> > (It was step 1 in this modified workflow that generated the issue)
>> >
>> > Mehul
>> > ps: the recon-all.log file from the error reported earlier is
>> attached
>> > for reference (i sent it to you but forgot to send it to the mailing
>> > list earlier)
>> >
>> >
>> >
>> >
>> > On Thu, May 30, 2013 at 8:31 AM, Z K
>> > > >
>>  > >
>> >>
>> wrote:
>> >
>> > Could you provide the recon-all.log file?
>> >
>> > -Zeke
>> >
>> > On 05/30/2013 10:24 AM, Gennan Chen wrote:
>> > > Does 5.3 assume recon-all -all will always run first? Since
>> > ribbon.mgz
>> > > will not get created till autorecon3. In V4, that is part of
>> > autorecon2
>> > > though.
>> > >
>> > > Gen
>> > >
>> > >
>> > > On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat
>> > mailto:mpsam...@gmail.com>
>> >
>> > > 
>> > > >
>> > > ps: i believe my error is the same as the one in this
>> thread:
>> > >
>> > >
>> > >
>> >
>> http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.**
>> edu/msg28047.html
>> > >
>> > >
>> > > Mehul
>> > >
>> > >
>> > > On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat
>> > mailto:mpsam...@gmail.com>
>> >
>> > > 
>> > > >
>> > > Hi Folks,
>

Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3

[Mehul Sampat]

Hi Doug,
Yes, we see the same error as in msg28047.html; here is the line from my
recon-all.log:

mghRead(/mnt/horizon/stage/HLC//004_151_3106223/WBS/Baseline/Freesurfer/mri/ribbon.mgz,
-1): could not open file

In msg28047.html, Milkos suggested that the issue could be the following
line in recon-all
"  set DoSegStats   = 1"

(in recon-all script in 5.2 this is line 5225; under the case "-autorecon2"
)
(in recon-all script in 5.3 this is line 5401; under the case "-autorecon2"
)

I think he is right; first i was confused why this issue was not seen with
-autrecon2-cp

because there is "  set DoSegStats   = 1"  for -autrecon2-cp too;
(in recon-all script in 5.3 this is line 5480; under the case
"-autorecon2-cp")

But normally we run -autorecon3 or -all before running -autorecon2-cp; so
in this case
the ribbon exists and the error does not show up with  -autorecon2-cp (if
-all or -autorecon3 is run before).

Mehul













On Tue, Jun 4, 2013 at 10:49 AM, Douglas N Greve
wrote:

> The error in  msg28047.html is that there was no ribbon.mgz. Is that the
> error you are receiving?
> 
> On 06/04/2013 01:45 PM, Mehul Sampat wrote:
> > Hi Zeke,
> > Thanks for looking into this; had a quick followup item to report.
> > So for the same subject  "recon-all -all" runs through smoothly;
> > (it was only recon-all -autorecon1 -autorecon2 that generated the error)
> >
> > I had not seen the error before since in the past, my workflow was as
> > follows:
> >
> > 1. run recon-all with -all
> > 2. add control points if required
> > 3. run recon-all with -autorecon2-cp and autorecon3
> >
> > This ran through without any errors;
> >
> > Now to save some processing time, the modified workflow is:
> > 1. run recon-all with -autorecon1 -autorecon2
> > 2. add control points if required
> > 3. run recon-all with -autorecon2-cp and autorecon3
> > (It was step 1 in this modified workflow that generated the issue)
> >
> > Mehul
> > ps: the recon-all.log file from the error reported earlier is attached
> > for reference (i sent it to you but forgot to send it to the mailing
> > list earlier)
> >
> >
> >
> >
> > On Thu, May 30, 2013 at 8:31 AM, Z K  > > wrote:
> >
> > Could you provide the recon-all.log file?
> >
> > -Zeke
> >
> > On 05/30/2013 10:24 AM, Gennan Chen wrote:
> > > Does 5.3 assume recon-all -all will always run first? Since
> > ribbon.mgz
> > > will not get created till autorecon3. In V4, that is part of
> > autorecon2
> > > though.
> > >
> > > Gen
> > >
> > >
> > > On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat
> > mailto:mpsam...@gmail.com>
> > > >> wrote:
> > >
> > > ps: i believe my error is the same as the one in this thread:
> > >
> > >
> > >
> >
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html
> > >
> > >
> > > Mehul
> > >
> > >
> > > On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat
> > mailto:mpsam...@gmail.com>
> > > >>
> wrote:
> > >
> > > Hi Folks,
> > > I am running recon-all with -autorecon1
> > > -autorecon2,  -nomotioncor -notal-check -nonuintensitycor
> > > (this is with fs version 5.3)
> > > it almost runs through but toward the end, when
> > mri_segstats is
> > > called I get the error message:
> > > .../mri/ribbon.mgz, -1): could not open file
> > > any ideas why this could be occurring ?
> > > Thanks
> > > Mehul
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> >  > >
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > The information in this e-mail is intended only for the
> > person to
> > > whom it is
> > > addressed. If you believe this e-mail was sent to you in
> > error and
> > > the e-mail
> > > contains patient information, please contact the Partners
> > Compliance
> > > HelpLine at
> > > http://www.partners.org/complianceline . If the e-mail was sent to
> > > you in error
> > > but does not contain patient information, please contact the
> > sender
> > > and properly
> > > dispose of the e-mail.
> > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 

Re: [Freesurfer] longer run time on 5.3 versus 5.2 ?

[Pedro Paulo de Magalhães Oliveira Junior]

I saw this issue too.

The total running time went from an average of 16.3h to 20.4h

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Tue, Jun 4, 2013 at 2:54 PM, Mehul Sampat  wrote:

> Hi Bruce,
>
> Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a
> big change to
> and are trying to isolate the root cause
>
> We are running  75 cases run with 5.3 that have been run with 5.2 before;
> once they are done, will let you all know if this issue is seen in other
> cases too.
> Mehul
> ps: the cases were run on different machines but the specs of the two
> machines are quite similar;
> we are also trying to see if it is hard-ware related..
>
>
>
>
> On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl 
> wrote:
>
>> Hi Mehul
>>
>> no, that's definitely not expected for it to go from 20 min to almost 5
>> hours! We'll investigate as that shouldn't be the case.
>> Bruce
>>
>>
>>
>> On Tue, 4 Jun 2013, Mehul Sampat wrote:
>>
>>  In some cases, we are seeing that, for the same subject, the run time is
>>> slower for 5.3 versus 5.2;
>>> A quick check on recon-all-status.log shows that the CA Reg Inv step is
>>> taking longer with 5.3.
>>>
>>> recon-all-status.log from data processed with 5.2:
>>>
>>> #@# CA Reg Thu Jan 17 16:03:53 PST 2013
>>> #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013
>>>
>>> recon-all-status.log from data processed with 5.3
>>>
>>> #@# CA Reg Mon Jun  3 19:46:37 PDT 2013
>>> #@# CA Reg Inv Tue Jun  4 04:52:57 PDT 2013
>>>
>>>  Is this expected ? Or in your own testing are the recon-all processing
>>> times similar for 5.2 versus 5.3 ? The recon-all.log
>>> file for both cases are attached;
>>> Thanks
>>> Mehul
>>>
>>>
>>>
>>>
>>
>> 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] longer run time on 5.3 versus 5.2 ?

[Bruce Fischl]

ok, thanks
On Tue, 4 Jun 2013, Mehul Sampat wrote:


Hi Bruce, 
Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a big 
change to 
and are trying to isolate the root cause

We are running  75 cases run with 5.3 that have been run with 5.2 before; 
once they are done, will let you all know if this issue is seen in other cases 
too. 
Mehul
ps: the cases were run on different machines but the specs of the two machines 
are quite similar; 
we are also trying to see if it is hard-ware related..




On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl  
wrote:
  Hi Mehul

  no, that's definitely not expected for it to go from 20 min to almost 5 
hours! We'll investigate as that shouldn't
  be the case.
  Bruce


  On Tue, 4 Jun 2013, Mehul Sampat wrote:

In some cases, we are seeing that, for the same subject, the run 
time is slower for 5.3 versus 5.2;  
A quick check on recon-all-status.log shows that the CA Reg Inv 
step is taking longer with 5.3.

recon-all-status.log from data processed with 5.2:

#@# CA Reg Thu Jan 17 16:03:53 PST 2013
#@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013

recon-all-status.log from data processed with 5.3

#@# CA Reg Mon Jun  3 19:46:37 PDT 2013
#@# CA Reg Inv Tue Jun  4 04:52:57 PDT 2013

 Is this expected ? Or in your own testing are the recon-all 
processing times similar for 5.2 versus 5.3
? The recon-all.log
file for both cases are attached;
Thanks
Mehul





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Re: [Freesurfer] longer run time on 5.3 versus 5.2 ?

[Mehul Sampat]

Hi Bruce,

Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a
big change to
and are trying to isolate the root cause

We are running  75 cases run with 5.3 that have been run with 5.2 before;
once they are done, will let you all know if this issue is seen in other
cases too.
Mehul
ps: the cases were run on different machines but the specs of the two
machines are quite similar;
we are also trying to see if it is hard-ware related..




On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl wrote:

> Hi Mehul
>
> no, that's definitely not expected for it to go from 20 min to almost 5
> hours! We'll investigate as that shouldn't be the case.
> Bruce
>
>
>
> On Tue, 4 Jun 2013, Mehul Sampat wrote:
>
>  In some cases, we are seeing that, for the same subject, the run time is
>> slower for 5.3 versus 5.2;
>> A quick check on recon-all-status.log shows that the CA Reg Inv step is
>> taking longer with 5.3.
>>
>> recon-all-status.log from data processed with 5.2:
>>
>> #@# CA Reg Thu Jan 17 16:03:53 PST 2013
>> #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013
>>
>> recon-all-status.log from data processed with 5.3
>>
>> #@# CA Reg Mon Jun  3 19:46:37 PDT 2013
>> #@# CA Reg Inv Tue Jun  4 04:52:57 PDT 2013
>>
>>  Is this expected ? Or in your own testing are the recon-all processing
>> times similar for 5.2 versus 5.3 ? The recon-all.log
>> file for both cases are attached;
>> Thanks
>> Mehul
>>
>>
>>
>>
>
> 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
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] Recon-all difficulties off-site

[Nitenson, Adam]

>
> Hi Doug,
>
> The command runs a bit further now but then exits with errors.
> Unfortunately this time there is no specific stated error. The last few
> lines of the log are:
>
> INFO: extension is mgz
> #
> #@# Talairach Tue Jun  4 13:22:08 EDT 2013
> /gpfs/data/twhite/anitenso/FreesurferPractice/unpack4/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
> --i orig.mgz --o orig_nu.mgz
>
> Linux node271 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29 UTC
> 2012 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s unpack4 exited with ERRORS at Tue Jun  4 13:22:10 EDT 2013
>
>
>
> The only other section of the log that seems like it could be related to
> an error is:
>
> Can't locate MNI/Startup.pm in @INC (@INC contains:
> /gpfs/runtime/opt/perl/5.16.0/lib
> /gpfs/runtime/opt/perl/5.16.0/lib/site_perl /usr/local/lib64/perl5
> /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at
> /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37.
> BEGIN failed--compilation aborted at
> /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37.
>
> So, I'm not sure what it's not liking here.
>
> Thanks again,
> Adam
>
>
> On Tue, Jun 4, 2013 at 11:44 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> That dcmunpack command will put the data into a file called
>> unpack3/MPRAGE/002/struct.nii
>> It needs to be put into upack3/mri/orig/002.mgz
>> doug
>>
>>
>>
>>
>> On 06/04/2013 11:22 AM, Nitenson, Adam wrote:
>>
>>> Hi Doug,
>>>
>>> When I try the command as you suggested:
>>> recon-all -all -s unpack3
>>> I get the following error:
>>>
>>> ERROR: no run data found in /gpfs/data/twhite/anitenso/**
>>> FreesurferPractice/unpack3/**mri. Make sure to
>>> have a volume called 001.mgz in  /gpfs/data/twhite/anitenso/**
>>> FreesurferPractice/unpack3/**mri/orig
>>>
>>> Do you know why I might be lacking that volume? This was not usually an
>>> issue after running the two unpacksdcmdir commands (for MPRAGE and bold
>>> runs).
>>>
>>> Thanks,
>>> Adam
>>>
>>>
>>> On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu 
>>> >
>>> wrote:
>>>
>>> Hi Adam, if the subject folder exists and you pass recon-all a -i
>>> flag,
>>> then it will exit with error saying that the data exist (otherwise it
>>> would overwrite what is there). However, just because the subject
>>> folder
>>> exists does not mean that there is any data sitting in
>>> subject/mri/orig.
>>> Then it will tell you that it cannot find any data.
>>>
>>> Note that when you run recon-all, you need to tell it to do something
>>> (eg, add the "-all" flag to do everything)
>>>
>>> doug
>>>
>>>
>>> On 06/03/2013 03:21 PM, Nitenson, Adam wrote:
>>> > Hello users,
>>> >
>>> > I am trying to get Freesurfer (5.2) working properly off-site and
>>> am
>>> > encountering errors I did not have while working at the Martinos
>>> > center. We use the same Siemens 3T Tim Trio scanner at Brown, so I
>>> > would hope the data is similar to work with.
>>> >
>>> > I have been using dcmunpack since unpacksdcmdir is not
>>> identifying the
>>> > DICOM files properly. I have successfully unpacked the
>>> structural and
>>> > bold scans using the command (entered from the raw scan data
>>> folder:
>>> >
>>> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3
>>> -run 2
>>> > MPRAGE nii struct (I also tried using mgz instead of nii,
>>> and also
>>> > changed struct to other things as it appears to be a naming
>>> argument)
>>> >
>>> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3
>>> -fsfast
>>> > -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii
>>> f.nii -run
>>> > 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9
>>> > bold nii f.nii
>>> >
>>> > (path) just being an abbreviate piece of the relevant pathway
>>> >
>>> > These generate the MPRAGE and bold folders in the subject folder as
>>> > expected. I have difficulties with the next commands
>>> (environment has
>>> > been set).
>>> >
>>> > I try:
>>> > recon-all -i  -s  -force
>>> > recon-all -i (path)/FreesurferPractice/**unpack/MPRAGE/002 -s
>>> unpack3
>>> > (I got an error about using -force so I omitted that from my
>>> command)
>>> >
>>> > and get the following Error
>>> > ERROR: You are trying to re-run an existing subject with (possibly)
>>> >  new input data (-i). If this is truly new input data, you
>>> should delete
>>> >  the subject folder and re-run, or specify a different subject
>>> name.
>>> >  If you are just continuing an analysis of an existing subject,
>>> then
>>> >  omit all -i flags.
>>> >
>>> > Yet

Re: [Freesurfer] SPM ROI to Cortical Thickness

[Douglas N Greve]

Make sure that your SPM volume is registered to the anatomical, then use 
mri_vol2surf to map the volume to the surface, then mri_segstats to 
extract the mean of the thickness

doug




On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote:
>
> main lab: (617) 355-0400

Dear FreeSurfer Experts,

I was wondering if anyone can advise on the best way to use an ROI mask 
created in SPM (XjView) to extract cortical thickness values in freesurfer.

Thank you in advance for your help!

Ola

Ola Ozranov-Palchik M.S.
Research Coordinator, Gaab Lab
Laboratories of Cognitive Neuroscience

Children's Hospital Boston
1 Autumn Street, Mailbox # 713
Boston, MA 02115
olga.ozra...@childrens.harvard.edu 

phone: (617) 334-5046
main lab: (617) 355-0400
fax: (617) 730-0518
http://www.childrenshospital.org/research/gaablab



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

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

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[Freesurfer] SPM ROI to Cortical Thickness

[Ozranov-Palchik, Ola]

Dear FreeSurfer Experts,

I was wondering if anyone can advise on the best way to use an ROI mask created 
in SPM (XjView) to extract cortical thickness values in freesurfer.

Thank you in advance for your help!
Ola


Ola Ozranov-Palchik M.S.
Research Coordinator, Gaab Lab
Laboratories of Cognitive Neuroscience
Children's Hospital Boston
1 Autumn Street, Mailbox # 713
Boston, MA 02115
olga.ozra...@childrens.harvard.edu
phone: (617) 334-5046
main lab: (617) 355-0400
fax: (617) 730-0518
http://www.childrenshospital.org/research/gaablab

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Re: [Freesurfer] mris_preproc --qdec-long problem

[Christopher McCarthy]

Dr. Reuter,

Thanks for your help, it got me through the error I was having.  On to the
next one:

When I enter the command:

mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage
--hemi lh --meas thickness --out lh.thickness.mgh

it spits out the following two lines before quitting:

nsubjects = 45
ERROR: cannot find /media/freesurfer/.long.

Any idea what I'm missing?

Thanks for your help and patience,

Chris


On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter
wrote:

> Hi Chris,
>
> this is a good question for the list (cc'ed), others may or will have the
> same problem.
>
> The problem is with your table file, specifically the new line character.
> DOS uses \r\n , Mac \r and Linux \n.
> Your text file uses \r, so it probably was created on a mac.
>
> The problem is that the "cat" command (at least in linux) does not work on
> your file:
> cat long.qdec.table.dat is empty
>
> You can convert the \r to \n (linux format):
>  tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat
>
> and then should be able to run the preproc command.
>
> People with DOS formats should not run the above "tr' command as they will
> end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat'
> directly (so there is no need)? If anyone on the list knows a good way of
> cat and awk a file independently of the new line (and working on all OS),
> let me know. This is the command I use:
>
> cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#")
> printf("%s.long.%s\n", $1, $2)}'
>
> to generate the subjects id's from the table's first two columns.
>
> Best, Martin
>
>
>
> On 06/03/2013 03:45 PM, Christopher McCarthy wrote:
>
>> Dr. Reuter,
>>
>> We corresponded in the past about QDEC, and you gave me great help.  The
>> lab I work for is now moving towards using the Longitudinal Mixed Effects
>> Model.  When I go to run the command:
>>
>> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target
>> study_average --hemi lh --meas thickness --out lh.thickness.mgh
>>
>> I get the error: 'ERROR: no subjects specified.'  I am attaching my
>> long.qdec.table.dat, which works fine when loaded by QDEC.  Do you have any
>> idea of why I am getting this error?
>>
>> Thanks,
>>
>> Chris McCarthy
>>
>
> --
> 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
>
>
>
> 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] longer run time on 5.3 versus 5.2 ?

[Bruce Fischl]

Hi Mehul

no, that's definitely not expected for it to go from 20 min to almost 5 
hours! We'll investigate as that shouldn't be the case.

Bruce


On Tue, 4 Jun 2013, Mehul Sampat wrote:


In some cases, we are seeing that, for the same subject, the run time is slower 
for 5.3 versus 5.2;  
A quick check on recon-all-status.log shows that the CA Reg Inv step is taking 
longer with 5.3.

recon-all-status.log from data processed with 5.2:

#@# CA Reg Thu Jan 17 16:03:53 PST 2013
#@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013

recon-all-status.log from data processed with 5.3

#@# CA Reg Mon Jun  3 19:46:37 PDT 2013
#@# CA Reg Inv Tue Jun  4 04:52:57 PDT 2013

 Is this expected ? Or in your own testing are the recon-all processing times 
similar for 5.2 versus 5.3 ? The recon-all.log
file for both cases are attached;
Thanks
Mehul


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[Freesurfer] mri_nu_correct.mni

[Cristian Paz]

Dear FreeSurfers!

I want to do bias correction on some T1 and T2 images.  I have heard that
you can do this by using mri_nu_correct.mni

how should I use this command?

I could not understand this (I am a beginner in FS) :
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni

would it be something like :
mri_nu_correct.mni -i  -o
?

Thank you very much!

Kind regards,
Cris
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Re: [Freesurfer] Freesurfer error..recon-all fails

[Manish Dalwani]

Sorry for the bunch of emails. I registered and got the license file. I have 
been using this software after a long time and feel silly that this was the 
thing that was causing trouble. Thank you Doug!
Manish



 From: Douglas N Greve 
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Tuesday, June 4, 2013 10:15 AM
Subject: Re: [Freesurfer] Freesurfer error..recon-all fails
 

Does the license fileexist? Note it is not called license.txt
On 06/04/2013 12:13 PM, Manish Dalwani wrote:
> Hello Freesurfer's
>
> I am working on the MAC OS 10.8 and just recently installed the 
> freesurfer on this server machine.
>
> I have checked the permissions to various and folders and they look ok 
> to me.
>
> When I run the following command:
> recon-all -i MR100021.dcm -s test2
>
> I get the following error
> server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
> /Applications/freesurfer/subjects/test2
> \n mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n
> mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/license.txt 
> not found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> --
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm...
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
>
> recon-all -s test2 exited with ERRORS at Tue Jun  4 09:56:10 MDT 2013
>
> For more details, see the log file 
> /Applications/freesurfer/subjects/test2/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> I am attaching the log file as well, and would appreciate if people 
> can help with this issue.
>
> Best Regards,
> Manish Dalwani
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] recon-all error

[Bruce Fischl]

Hi Rafa

this doesn't look like the whole subject dir, just some files from it 
(e.g. no mri/transforms/talairach.xfm). Don't email it to me - use our 
ftp site


cheers
Bruce
On Tue, 4 Jun 2013, Rafa X wrote:


Hi Bruce,Thanks for your reply. I have attached the zipped subject dir (please, 
note that I had to compress it twice for sending
problems).
Rafa.


2013/6/4 Bruce Fischl 
  Hi Rafa

  that sounds like a bug. Can you gzip and upload the whole subject dir?

  cheers
  Bruce
  On Tue, 4 Jun 2013, Rafa X wrote:

Dear freesurfer experts,

I was running an autorecon2 in the recon-all but always gives me 
this memory allocation error, only on
this
subject. Im using FS v5.1



#@# ASeg Stats Mon Jun  3 20:13:11 CEST 2013
/root/trabajo/freesurfer/subjects/qsm1_17_stats2_g

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --excludeid 0
--excl-ctxgmwm
--supratent --subcortgray --in mri/norm.mgz --in-intensity-name 
norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --ctab 
/root/trabajo/freesurfer/ASegStatsLUT.txt --subject
qsm1_17_stats2_g


$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --excludeid 0
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units
MR
--etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab 
/root/trabajo/freesurfer/ASegStatsLUT.txt
--subject
qsm1_17_stats2_g
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     root
atlas_icv (eTIV) = 1196346 mm^3    (det: 1.628380 )
Loading mri/aseg.mgz
Getting Cerebral WM volumes from surface
lh white matter volume 206011
rh white matter volume 198149
Getting Cerebral GM and WM volumes from surfaces
lh surface-based volumes (mm3): wTot = 235659.045132,  pTot = 
416409.266434 c = 180750.221302
rh surface-based volumes (mm3): wTot = 223785.748405,  pTot = 
402494.420361 c = 178708.671956
MRIalloc: could not allocate 540094766 frames

Computing SupraTentVolCor
Cannot allocate memory
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 
06:23:23 GMT 2006 x86_64 x86_64 x86_64
GNU/Linux

recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun  3 
20:18:36 CEST 2013

For more details, see the log file

/root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Any help will be appreaciated,

Many thanks in advance
Rafa




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Re: [Freesurfer] Freesurfer error..recon-all fails

[Manish Dalwani]

Ok I checked the other version of freesurfer and I do have .license file in the 
freesurfer folder. How can I get this file? 

Best,
Manish



 From: Douglas N Greve 
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Tuesday, June 4, 2013 10:15 AM
Subject: Re: [Freesurfer] Freesurfer error..recon-all fails
 

Does the license fileexist? Note it is not called license.txt
On 06/04/2013 12:13 PM, Manish Dalwani wrote:
> Hello Freesurfer's
>
> I am working on the MAC OS 10.8 and just recently installed the 
> freesurfer on this server machine.
>
> I have checked the permissions to various and folders and they look ok 
> to me.
>
> When I run the following command:
> recon-all -i MR100021.dcm -s test2
>
> I get the following error
> server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
> /Applications/freesurfer/subjects/test2
> \n mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n
> mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/license.txt 
> not found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> --
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm...
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
>
> recon-all -s test2 exited with ERRORS at Tue Jun  4 09:56:10 MDT 2013
>
> For more details, see the log file 
> /Applications/freesurfer/subjects/test2/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> I am attaching the log file as well, and would appreciate if people 
> can help with this issue.
>
> Best Regards,
> Manish Dalwani
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] Freesurfer error..recon-all fails

[Manish Dalwani]

yes, there is a file called LICENSE in the freesurfer folder. Should I look for 
something else?
Thanks,
Manish



 From: Douglas N Greve 
To: freesurfer@nmr.mgh.harvard.edu 
Sent: Tuesday, June 4, 2013 10:15 AM
Subject: Re: [Freesurfer] Freesurfer error..recon-all fails
 

Does the license fileexist? Note it is not called license.txt
On 06/04/2013 12:13 PM, Manish Dalwani wrote:
> Hello Freesurfer's
>
> I am working on the MAC OS 10.8 and just recently installed the 
> freesurfer on this server machine.
>
> I have checked the permissions to various and folders and they look ok 
> to me.
>
> When I run the following command:
> recon-all -i MR100021.dcm -s test2
>
> I get the following error
> server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
> /Applications/freesurfer/subjects/test2
> \n mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n
> mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/license.txt 
> not found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> --
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm...
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
>
> recon-all -s test2 exited with ERRORS at Tue Jun  4 09:56:10 MDT 2013
>
> For more details, see the log file 
> /Applications/freesurfer/subjects/test2/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> I am attaching the log file as well, and would appreciate if people 
> can help with this issue.
>
> Best Regards,
> Manish Dalwani
>
>
> ___
> 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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LICENSE
Description: Binary data
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Freesurfer error..recon-all fails

[Douglas N Greve]

Does the license fileexist? Note it is not called license.txt
On 06/04/2013 12:13 PM, Manish Dalwani wrote:
> Hello Freesurfer's
>
> I am working on the MAC OS 10.8 and just recently installed the 
> freesurfer on this server machine.
>
> I have checked the permissions to various and folders and they look ok 
> to me.
>
> When I run the following command:
> recon-all -i MR100021.dcm -s test2
>
> I get the following error
> server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
> /Applications/freesurfer/subjects/test2
> \n mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n
> mri_convert 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
> /Applications/freesurfer/subjects/test2/mri/orig/001.mgz
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/license.txt 
> not found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> --
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm...
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
>
> recon-all -s test2 exited with ERRORS at Tue Jun  4 09:56:10 MDT 2013
>
> For more details, see the log file 
> /Applications/freesurfer/subjects/test2/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> I am attaching the log file as well, and would appreciate if people 
> can help with this issue.
>
> Best Regards,
> Manish Dalwani
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] v 5.3 pial- FLAIR vs T2

[Bruce Fischl]

Hi Octavian

not sure what  eT2W FLAIR sense is. The T2_SPACE flair is the only one 
that we have routinely used that has about 1mm isotropic resolution, and 
yes we will take care of the registration. Whatever FLAIR you use just 
point FreeSurfer at it (nifti or dicom)


cheers
Bruce


On Tue, 4 Jun 2013, octavian lie wrote:


Dear All,
 
Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably used 
as auxiliary for pial definition?
Does Freesurfer take care of coregistration between these and the MPRAGE?
What would be the command line (Linux Ubuntu) if I want to use SPM generated 
nifti DICOM concatenations for the T2 or FLAIR,
instead of native DICOMs?
Thank you,
 
Octavian

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[Freesurfer] Freesurfer error..recon-all fails

[Manish Dalwani]

Hello Freesurfer's

I am working on the MAC OS 10.8 and just recently installed the freesurfer on 
this server machine. 

I have checked the permissions to various and folders and they look ok to me. 

When I run the following command:
recon-all -i MR100021.dcm -s test2

I get the following error 
server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s test2
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 
13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
/Applications/freesurfer/subjects/test2
\n mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
/Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n
mri_convert /Applications/freesurfer/subjects/anat_5214/MR100021.dcm 
/Applications/freesurfer/subjects/test2/mri/orig/001.mgz 
--
ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm...
Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 
13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s test2 exited with ERRORS at Tue Jun  4 09:56:10 MDT 2013

For more details, see the log file 
/Applications/freesurfer/subjects/test2/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


I am attaching the log file as well, and would appreciate if people can help 
with this issue. 

Best Regards,
Manish Dalwani

recon-all.log
Description: Binary data
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Re: [Freesurfer] motioncor

[Bruce Fischl]

isn't that a feature? Freeview saves state to try to preserve the 
appropriate settings.

As for recon-all, yes that is the way it works. If you want to start with a 
new volume with -i you have to delete the subject dir (or specify a newly 
named one)

cheers
Bruce


On Tue, 4 Jun 
2013, 
obre...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> This is certainly something I want to avoid, I guess I won't be using the
> -motioncor flag in any of my studies!
>
> I ran recon-all using both only one and two (motion corrected and
> averaged) source volumes, and the results do seem to suggest that using
> one vs. two volumes is an empirical issue. In the former case, I tried
> using the -i switch to point to a specific source volume (as you
> suggested), but failed to do so for I had already created the subjects'
> folders. Therefore, in order to use a single source volume, I had to move
> the remaining ones outside their corresponding mri/orig/ folders. Is there
> a way around this?
>
> I also started using Freeview and I'm finally being able to display the
> raw volumes "cleanly". However, I want to find out why is it that when you
> change the contrast of your volumes, and avoid saving these changes, every
> time you reload the volumes they're displayed using the contrast settings
> you last employed? Why aren't these settings reset to their default
> values?
>
> Thanks!
>
> --G
>
>
>> if they are named orig/00[012345].mgz then I think they will be averaged
>> but without motion correction, which is almost certainly not what you want
>>
>> On Sun, 2 Jun 2013,
>> obre...@nmr.mgh.harvard.edu wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks for responding! For the sake of clarification, let's say I have
>>> multiple source volumes (XXX.mgz) in mri/orig/, and I don't use the -i
>>> switch in recon-all to point to one of them, exclusively. If I
>>> additionally include the -nomotioncor option, will the multiple source
>>> volumes be averaged without correcting for motion between them, yielding
>>> orig.mgz as output?
>>>
>>> Best,
>>>
>>> Gabriel
>>>
>>>
 Hi Gabriel

 if you want to process only one volume, then point recon-all at it with
 the -i switch. You can also use freeview instead of tkmedit for
 browsing
 the volumes - it's much more flexible.

 The two volumes vs. one is an empirical question. I've found that a
 single
 high-quality volume is better than motion-correcting and averaging two,
 particularly if one of the two is lower quality, but that's an ad hoc
 assessment on my part and depends a lot on field strength, coil,
 subject
 motion, etc

 cheers
 Bruce

 On Sun, 2 Jun 2013, Gabriel Obregon
 wrote:

> Hi,
>
> Could someone please help me with the following concerns:
>
> A. If I have multiple source volumes in mri/orig/ and run recon-all
> using the -nomotioncor option, how are these inputs processed compared
> to the case in which motion correction is employed, and what should I
> expect as my output?
>
> B. If I want to process only one of the multiple source volumes, i.e.,
> the "best", how should I proceed?
>
> C. I've been encountering displaying issues of the raw volumes using
> tkmedit. What other interfaces are readily available for browsing
> through the source volumes in order to assess their quality?
>
> D. Finally, if in one of my studies I could afford running only two
> MPRAGE sessions per subject, is motion correction advisable for
> segmenting the surfaces?
>
> Thanks!
>
> Gabriel
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>



>>>
>>>
>>>
>>
>>
>>
>
>
>
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[Freesurfer] v 5.3 pial- FLAIR vs T2

[octavian lie]

Dear All,

Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably
used as auxiliary for pial definition?
Does Freesurfer take care of coregistration between these and the MPRAGE?
What would be the command line (Linux Ubuntu) if I want to use SPM
generated nifti DICOM concatenations for the T2 or FLAIR, instead of native
DICOMs?
Thank you,

Octavian
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Re: [Freesurfer] Recon-all difficulties off-site

[Douglas N Greve]

That dcmunpack command will put the data into a file called 
unpack3/MPRAGE/002/struct.nii
It needs to be put into upack3/mri/orig/002.mgz
doug



On 06/04/2013 11:22 AM, Nitenson, Adam wrote:
> Hi Doug,
>
> When I try the command as you suggested:
> recon-all -all -s unpack3
> I get the following error:
>
> ERROR: no run data found in 
> /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. Make sure to
> have a volume called 001.mgz in 
>  /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/orig
>
> Do you know why I might be lacking that volume? This was not usually 
> an issue after running the two unpacksdcmdir commands (for MPRAGE and 
> bold runs).
>
> Thanks,
> Adam
>
>
> On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Adam, if the subject folder exists and you pass recon-all a -i
> flag,
> then it will exit with error saying that the data exist (otherwise it
> would overwrite what is there). However, just because the subject
> folder
> exists does not mean that there is any data sitting in
> subject/mri/orig.
> Then it will tell you that it cannot find any data.
>
> Note that when you run recon-all, you need to tell it to do something
> (eg, add the "-all" flag to do everything)
>
> doug
>
>
> On 06/03/2013 03:21 PM, Nitenson, Adam wrote:
> > Hello users,
> >
> > I am trying to get Freesurfer (5.2) working properly off-site and am
> > encountering errors I did not have while working at the Martinos
> > center. We use the same Siemens 3T Tim Trio scanner at Brown, so I
> > would hope the data is similar to work with.
> >
> > I have been using dcmunpack since unpacksdcmdir is not
> identifying the
> > DICOM files properly. I have successfully unpacked the
> structural and
> > bold scans using the command (entered from the raw scan data folder:
> >
> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2
> > MPRAGE nii struct (I also tried using mgz instead of nii,
> and also
> > changed struct to other things as it appears to be a naming
> argument)
> >
> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast
> > -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii
> f.nii -run
> > 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9
> > bold nii f.nii
> >
> > (path) just being an abbreviate piece of the relevant pathway
> >
> > These generate the MPRAGE and bold folders in the subject folder as
> > expected. I have difficulties with the next commands
> (environment has
> > been set).
> >
> > I try:
> > recon-all -i  -s  -force
> > recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3
> > (I got an error about using -force so I omitted that from my
> command)
> >
> > and get the following Error
> > ERROR: You are trying to re-run an existing subject with (possibly)
> >  new input data (-i). If this is truly new input data, you
> should delete
> >  the subject folder and re-run, or specify a different subject name.
> >  If you are just continuing an analysis of an existing subject, then
> >  omit all -i flags.
> >
> > Yet when I omit -i and just use "recon-all -s unpack3", I get
> "ERROR:
> > nothing to do"
> >
> > I tried a different tactic and used
> >
> > "recon-all -s unpack3 -autorecon1" as well as "recon-all
> > -autorecon-all -s unpack3"
> >
> > which both created the various folders (bem, label, mri, surf, etc)
> > but failed with
> > "ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri.
> > Make sure to have a volume called 001.mgz in
> > (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run
> > of data call it 002.mgz, etc."
> >
> > I have tried these commands in both bash and tcsh shells with
> the same
> > effect. So the problem, it seems, is that my "mri" file is
> blank, and
> > this was not a problem I had running these commands at Martinos. Any
> > idea what the issue might be?
> >
> > Best,
> >
> > Adam Nitenson
> > Neuroscience Graduate Program
> > Laboratory of Affective Neuroscience
> > Brown University
> >
> >
> >
> > ___
> > 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
> 
> File

Re: [Freesurfer] motioncor

[obregon]

Hi Bruce,

This is certainly something I want to avoid, I guess I won't be using the
-motioncor flag in any of my studies!

I ran recon-all using both only one and two (motion corrected and
averaged) source volumes, and the results do seem to suggest that using
one vs. two volumes is an empirical issue. In the former case, I tried
using the -i switch to point to a specific source volume (as you
suggested), but failed to do so for I had already created the subjects'
folders. Therefore, in order to use a single source volume, I had to move
the remaining ones outside their corresponding mri/orig/ folders. Is there
a way around this?

I also started using Freeview and I'm finally being able to display the
raw volumes "cleanly". However, I want to find out why is it that when you
change the contrast of your volumes, and avoid saving these changes, every
time you reload the volumes they're displayed using the contrast settings
you last employed? Why aren't these settings reset to their default
values?

Thanks!

--G


> if they are named orig/00[012345].mgz then I think they will be averaged
> but without motion correction, which is almost certainly not what you want
>
> On Sun, 2 Jun 2013,
> obre...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Thanks for responding! For the sake of clarification, let's say I have
>> multiple source volumes (XXX.mgz) in mri/orig/, and I don't use the -i
>> switch in recon-all to point to one of them, exclusively. If I
>> additionally include the -nomotioncor option, will the multiple source
>> volumes be averaged without correcting for motion between them, yielding
>> orig.mgz as output?
>>
>> Best,
>>
>> Gabriel
>>
>>
>>> Hi Gabriel
>>>
>>> if you want to process only one volume, then point recon-all at it with
>>> the -i switch. You can also use freeview instead of tkmedit for
>>> browsing
>>> the volumes - it's much more flexible.
>>>
>>> The two volumes vs. one is an empirical question. I've found that a
>>> single
>>> high-quality volume is better than motion-correcting and averaging two,
>>> particularly if one of the two is lower quality, but that's an ad hoc
>>> assessment on my part and depends a lot on field strength, coil,
>>> subject
>>> motion, etc
>>>
>>> cheers
>>> Bruce
>>>
>>> On Sun, 2 Jun 2013, Gabriel Obregon
>>> wrote:
>>>
 Hi,

 Could someone please help me with the following concerns:

 A. If I have multiple source volumes in mri/orig/ and run recon-all
 using the -nomotioncor option, how are these inputs processed compared
 to the case in which motion correction is employed, and what should I
 expect as my output?

 B. If I want to process only one of the multiple source volumes, i.e.,
 the "best", how should I proceed?

 C. I've been encountering displaying issues of the raw volumes using
 tkmedit. What other interfaces are readily available for browsing
 through the source volumes in order to assess their quality?

 D. Finally, if in one of my studies I could afford running only two
 MPRAGE sessions per subject, is motion correction advisable for
 segmenting the surfaces?

 Thanks!

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



>>>
>>>
>>>
>>
>>
>>
>
>
>

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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info
doug

On 06/04/2013 09:11 AM, Glen Lee wrote:
> Hi Doug,
> I tried as you suggested, but i've got the following error: 
>  e.g.,cannot find any csd files.
> However, I can see them stored in csd folder as shown below:
>
> /2D/results/LH/GLM/csd> ls
> mc-z.negative.j001-osgm.csd  perm.abs.2.j001-osgm.csd
>
> I'm guessing that I need to define the path for this csd folder?
>
>  Here is the command line that I typed in:
>  mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim  --overwrite
>
>  -Glen
>
>
>
>
>
>
>
>
> On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> hi Glen, no cluster will show up if the p-value for all clusters
> is above .05. You can change this with --cwpvalthresh to something
> like .99. That should give you all the clusters. Also, you don't
> have to run the full simulation again; you can use the --no-sim
> option and it will use the simulation that you already did.
> doug
>
>
>
> On 6/3/13 9:45 PM, Glen Lee wrote:
>> Indeed, I initially tried 10,000 iterations and got nothing.
>> What else then could have gone wrong?
>>
>> FYI, I use v5.1.0.
>>
>>
>> On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> You will need more like 1 iterations instead of 100.
>> doug
>>
>> On 06/03/2013 04:49 PM, Glen Lee wrote:
>> > Hello Freesurfer experts--
>> >
>> > I ran mri_glmfit-sim to validate the group level GLM result
>> (which was
>> > already done using mri_glmfit), but I was not able to get
>> any result
>> > out of it.
>> >
>> >  Even with a quite liberal threshold (2), no vertices came
>> out (below
>> > is what I typed in for the random permutation).
>> >
>> >  mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2
>>  --sim-sign
>> > abs --overwrite
>> >
>> > What is strange is that I was clearly see a number of
>> clusters when I
>> > overlaid sig.mgh at a matched threshold (e.g., p>2), but no
>> cluster
>> > shows up in  perm.abs.2.sig.cluster.mgh.
>> > I should be able to see the identical map between those right?
>> >
>> > FYI, I also pasted the content in
>> perm.abs.2.sig.cluster.summary below.
>> > As can be seen, nothing is listed in the stats table.
>> >
>> > Any of your help would be greatly appreciated.
>> > -Glen
>> >
>> >
>> >
>> >
>> >
>> >
>> > # Cluster Growing Summary (mri_surfcluster)
>> > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36
>> greve Exp $
>> > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
>> > # CreationTime 2013/06/03-20:19:31-GMT
>> > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
>> > GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
>> > GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
>> > GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
>> > GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
>> > GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
>> > GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
>> > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
>> > GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
>> > # cwd /glen/2D/results/LH
>> > # sysname  Linux
>> > # hostname sumo.uphs.upenn.edu 
>> 
>> > # machine  x86_64
>> > # FixVertexAreaFlag 1
>> > # FixSurfClusterArea 1
>> > #
>> > # Input  GLM/osgm/sig.mgh
>> > # Frame Number  0
>> > # srcsubj fsaverage_sym
>> > # hemi lh
>> > # surface white
>> > # annot aparc
>> > # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
>> > # SearchSpace_mm2 59961.4
>> > # SearchSpace_vtx 82070
>> > # Bonferroni 0
>> > # Minimum Threshold 2
>> > # Maximum Threshold infinity
>> > # Threshold Signabs
>> > # AdjustThreshWhenOneTail 1
>> > # CW PValue Threshold: 0.05
>> > # Area Threshold0 mm^2
>> > # CSD thresh  2.00
>> > # CSD nreps100
>> > # CSD simtype  perm
>> > # CSD contrast osgm
>> > # CSD confint  90.00
>> > # Overall max 3.495 at vertex 61659
>> > # Overall min -4.18843 at vertex 73402
>> > # NClusters  0
>> > # Total Cortical Surface Area 59961.4 (mm^2)
>> > # FixMNI = 0
>> > #
>> > # ClusterNo  Max   VtxMax Size(mm^2)  MNIX   MNIY   MNIZ  CWP
>> >  CWPLowCWPHi   NV

Re: [Freesurfer] Recon-all difficulties off-site

[Nitenson, Adam]

Hi Doug,

When I try the command as you suggested:
recon-all -all -s unpack3
I get the following error:

ERROR: no run data found in
/gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. Make sure to
have a volume called 001.mgz in
 /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/orig

Do you know why I might be lacking that volume? This was not usually an
issue after running the two unpacksdcmdir commands (for MPRAGE and bold
runs).

Thanks,
Adam


On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve
wrote:

> Hi Adam, if the subject folder exists and you pass recon-all a -i flag,
> then it will exit with error saying that the data exist (otherwise it
> would overwrite what is there). However, just because the subject folder
> exists does not mean that there is any data sitting in subject/mri/orig.
> Then it will tell you that it cannot find any data.
>
> Note that when you run recon-all, you need to tell it to do something
> (eg, add the "-all" flag to do everything)
>
> doug
>
>
> On 06/03/2013 03:21 PM, Nitenson, Adam wrote:
> > Hello users,
> >
> > I am trying to get Freesurfer (5.2) working properly off-site and am
> > encountering errors I did not have while working at the Martinos
> > center. We use the same Siemens 3T Tim Trio scanner at Brown, so I
> > would hope the data is similar to work with.
> >
> > I have been using dcmunpack since unpacksdcmdir is not identifying the
> > DICOM files properly. I have successfully unpacked the structural and
> > bold scans using the command (entered from the raw scan data folder:
> >
> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2
> > MPRAGE nii struct (I also tried using mgz instead of nii, and also
> > changed struct to other things as it appears to be a naming argument)
> >
> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast
> > -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run
> > 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9
> > bold nii f.nii
> >
> > (path) just being an abbreviate piece of the relevant pathway
> >
> > These generate the MPRAGE and bold folders in the subject folder as
> > expected. I have difficulties with the next commands (environment has
> > been set).
> >
> > I try:
> > recon-all -i  -s  -force
> > recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3
> > (I got an error about using -force so I omitted that from my command)
> >
> > and get the following Error
> > ERROR: You are trying to re-run an existing subject with (possibly)
> >  new input data (-i). If this is truly new input data, you should delete
> >  the subject folder and re-run, or specify a different subject name.
> >  If you are just continuing an analysis of an existing subject, then
> >  omit all -i flags.
> >
> > Yet when I omit -i and just use "recon-all -s unpack3", I get "ERROR:
> > nothing to do"
> >
> > I tried a different tactic and used
> >
> > "recon-all -s unpack3 -autorecon1" as well as "recon-all
> > -autorecon-all -s unpack3"
> >
> > which both created the various folders (bem, label, mri, surf, etc)
> > but failed with
> > "ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri.
> > Make sure to have a volume called 001.mgz in
> > (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run
> > of data call it 002.mgz, etc."
> >
> > I have tried these commands in both bash and tcsh shells with the same
> > effect. So the problem, it seems, is that my "mri" file is blank, and
> > this was not a problem I had running these commands at Martinos. Any
> > idea what the issue might be?
> >
> > Best,
> >
> > Adam Nitenson
> > Neuroscience Graduate Program
> > Laboratory of Affective Neuroscience
> > Brown University
> >
> >
> >
> > ___
> > 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.
>
>
___

Re: [Freesurfer] mri_convert mgz to nifti

[Ray, Siddharth]

Thanks!!

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Tuesday, June 04, 2013 9:51 AM
To: Ray, Siddharth
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert mgz to nifti

mri_convert file.mgz file.nii.gz

should do the trick
On Tue, 4 Jun 2013, Ray, Siddharth wrote:

> 
> Hi all,
> 
>  
> 
> I just want to convert .mgz files to .nifti using mri_convert, do I 
> have to flip my image when I do that using RAS ? or I should simply use:
> 
>  
> 
> Mri_convert  input_file_name.mgz  output_file_name.nii
> 
>  
> 
>  
> 
> Thanks in advance,
> 
> Siddharth
> 
> 
>


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_convert mgz to nifti

[Rudolph Pienaar]

The command is 'mri_convert' not 'Mri_convert'  -- at least on case 
sensitive filesystems (like Linux and some-but-not-all Mac OS X).

On 6/4/13 10:46 , Ray, Siddharth wrote:
>
> Hi all,
>
> I just want to convert .mgz files to .nifti using mri_convert, do I 
> have to flip my image when I do that using RAS ? or I should simply use:
>
> Mri_convert  input_file_name.mgz  output_file_name.nii
>
> Thanks in advance,
>
> Siddharth
>
>
>
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-- 
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA

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Re: [Freesurfer] mri_convert mgz to nifti

[Bruce Fischl]

mri_convert file.mgz file.nii.gz

should do the trick
On Tue, 4 Jun 2013, Ray, Siddharth wrote:



Hi all,

 

I just want to convert .mgz files to .nifti using mri_convert, do I have to 
flip my image when I do that using RAS ? or I should
simply use:

 

Mri_convert  input_file_name.mgz  output_file_name.nii

 

 

Thanks in advance,

Siddharth


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[Freesurfer] mri_convert mgz to nifti

[Ray, Siddharth]

Hi all,

I just want to convert .mgz files to .nifti using mri_convert, do I have to 
flip my image when I do that using RAS ? or I should simply use:

Mri_convert  input_file_name.mgz  output_file_name.nii


Thanks in advance,
Siddharth
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[Freesurfer] Fwd: [All] freesurfer and centos6 updates!

[Emily Boeke]

Hi all,

I would like to save copy of the CentOS5 release of Freesurfer in my group's 
work space as described in the email below. The link in the email that is 
supposed to explain this doesn't work; could someone please let me know how to 
do this or point me to another webpage that explains it?

Thanks!

Emily

Begin forwarded message:

> From: Nick Schmansky 
> Subject: [All] freesurfer and centos6 updates!
> Date: December 10, 2012 4:08:30 PM EST
> To: a...@nmr.mgh.harvard.edu
> Cc: Martinos-tech , Help 
> 
> 
> 
> WARNING! The default Freesurfer version that runs on CentOS6 machines is
> going to change next Monday the 17th to a new CentOS6 specific version.
> 
> Right now at the Martinos Center we have a mix of CentOS4, CentOS5 and
> CentOS6 machines at the center.  All these currently use a version of
> freesurfer built on CentOS4 for maximum compatibility.  However, this
> means those users with CentOS6 systems are using a version that is
> slower than they could be using if properly optimized.
> 
> It is time for users of CentOS6 system to no longer be held back by the
> older systems.  So on next Monday the 17th, the default Freesufer on all
> CentOS6 systems (which includes launchpad, tensor, and the icepuffs)
> will be updated to a new CentOS6-specific build.
> 
> The mixed environment this results in can result in confusion for groups
> with a mix of CentOS versions among their workstations. To avoid this
> your group should do one of the following:
> 
>   (1) contact the Martinos IT Help Desk to upgrade your old CentOS4
>and CentOS5 systems to CentOS6. Sometime in the near
>future we will drop support all together for the old systems.
> 
>   (2) make a copy of the current CentOS4 release for your study into
>your group's work area and point your users' environments to
>use that copy.  This is what is recommended for study
>consistancy anyway and instructions can be found on the wiki at
> 
> http://surfer.nmr.mgh.harvard.edu/fswiki/MakingPrivateCopiesOfDistributions
> 
> NOTES:
> 
>   (1) to tell what CentOS version your workstation is running, run
> on it:
> 
>cat /etc/redhat-release
> 
>   (2) you are using the default freesurfer release if your PATH has 
>   in it directories that start with /usr/local/freesurfer. 
>This is a symlink that currently points to the CentOS4 release
>on all Linux machines at the center but will change to point at
>the CentOS6 release on all CentOS6 machines next Monday, the
>17th.
> 
> Feel free to email me with questions.
> 
> Nick Schmansky
> 
> 
> 
> 
> 
> 
> ___
> All mailing list
> a...@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all
> 
> 

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Re: [Freesurfer] hippocampal subfield segmentation

[Juan Eugenio Iglesias]

I would probably leave out the fissure, but not the fimbria...
Cheers,
/Eugenio

On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote:
> Hi guys!
> I have a dataset including hippocampal subfields obtained through the
> -hippo-subfields flag. I want to have a measure of total hippo volume
> and I'm not sure  which structures should I include in the sum. I was
> thinking to exclude fimbria and fissure and sum the others. Am I
> right? Or should I simply sum all the structures?
> Any help is more than welcome
> Cheers,
> Fabrizio
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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] error in 5.3

[Welsh, Robert]

hi bruce,

thanks. from the reading of "recon-all" it looks like this is a failure is
occurring in the latter part of autorecon3 so I'm just rerunning that set
and skipping autorecon2 on the subjects that failed.

correct?

best,

-robert


On 6/4/13 9:38 AM, "Bruce Fischl"  wrote:

p.s. you can check to see if those labels exist in your fsaverage/label
dir
On Tue, 4 Jun 2013, Welsh, Robert wrote:

> ah, that probably got there from the 5.2 recon-all. I'll go in and
> manually change those.
>
> thanks
>
> -robert
>
>
> On 6/4/13 8:59 AM, "Bruce Fischl"  wrote:
>
> Hi Robert
>
> I think you need to symlink the fsaverage dir to the 5.3 fsaverage
> instead of 5.2
>
> cheers
> Bruce
> On Tue, 4 Jun 2013, Welsh, Robert wrote:
>
>> Hi,
>>
>> We were re-processing a subject to test the fix for 5.2 to 5.3. The
>> initial recon-all and subsequent autrecon2
>> and autorecon3 were run a few days ago under 5.2. Yesterday I installed
>> 5.3 and we ran the following:
>>
>> export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer
>> recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
>>
>> It ran for about 4.5 hours and then gave this error:
>>
>>
>> 
>>-
>>-
>> -
>> [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log
>> SUBJECTS_DIR/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer
>> FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4
>> Loading source label.
>> Invalid argument
>> ERROR reading
>> 
>>/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh
>>.
>> label
>> Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24
>> 19:32:05 EDT 2008 x86_64 x86_64 x86_64
>> GNU/Linux
>>
>> recon-all -s s_ALS51 exited with ERRORS at Mon Jun  3 18:32:01 EDT 2013
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>> 
>>-
>>-
>> -
>>
>> Some help would be appreciated. There is a file lh.BA1.label but not
>> lh.BA1.thresh.label, indeed there are no
>> files with "thresh" in their name under that subject.
>>
>> Thanks!
>>
>> -Robert
>>
>> **
>> Electronic Mail is not secure, may not be read every day, and should not
>> be used for urgent or sensitive issues
>>
>>
>>
>
>
> 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
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> dispose of the e-mail.
>
> **
> Electronic Mail is not secure, may not be read every day, and should not
>be used for urgent or sensitive issues
>
>
>
>

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Re: [Freesurfer] error in 5.3

[Bruce Fischl]

p.s. you can check to see if those labels exist in your fsaverage/label 
dir
On Tue, 4 Jun 2013, Welsh, Robert wrote:

> ah, that probably got there from the 5.2 recon-all. I'll go in and
> manually change those.
>
> thanks
>
> -robert
>
>
> On 6/4/13 8:59 AM, "Bruce Fischl"  wrote:
>
> Hi Robert
>
> I think you need to symlink the fsaverage dir to the 5.3 fsaverage
> instead of 5.2
>
> cheers
> Bruce
> On Tue, 4 Jun 2013, Welsh, Robert wrote:
>
>> Hi,
>>
>> We were re-processing a subject to test the fix for 5.2 to 5.3. The
>> initial recon-all and subsequent autrecon2
>> and autorecon3 were run a few days ago under 5.2. Yesterday I installed
>> 5.3 and we ran the following:
>>
>> export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer
>> recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
>>
>> It ran for about 4.5 hours and then gave this error:
>>
>>
>> --
>> -
>> [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log
>> SUBJECTS_DIR/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer
>> FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4
>> Loading source label.
>> Invalid argument
>> ERROR reading
>> /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.
>> label
>> Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24
>> 19:32:05 EDT 2008 x86_64 x86_64 x86_64
>> GNU/Linux
>>
>> recon-all -s s_ALS51 exited with ERRORS at Mon Jun  3 18:32:01 EDT 2013
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>> --
>> -
>>
>> Some help would be appreciated. There is a file lh.BA1.label but not
>> lh.BA1.thresh.label, indeed there are no
>> files with "thresh" in their name under that subject.
>>
>> Thanks!
>>
>> -Robert
>>
>> **
>> Electronic Mail is not secure, may not be read every day, and should not
>> be used for urgent or sensitive issues
>>
>>
>>
>
>
> 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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> used for urgent or sensitive issues
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>
>
>
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Re: [Freesurfer] error in 5.3

[Bruce Fischl]

ok, let us know if it fixes your problem
Bruce
On Tue, 4 Jun 2013, Welsh, Robert 
wrote:

> ah, that probably got there from the 5.2 recon-all. I'll go in and
> manually change those.
>
> thanks
>
> -robert
>
>
> On 6/4/13 8:59 AM, "Bruce Fischl"  wrote:
>
> Hi Robert
>
> I think you need to symlink the fsaverage dir to the 5.3 fsaverage
> instead of 5.2
>
> cheers
> Bruce
> On Tue, 4 Jun 2013, Welsh, Robert wrote:
>
>> Hi,
>>
>> We were re-processing a subject to test the fix for 5.2 to 5.3. The
>> initial recon-all and subsequent autrecon2
>> and autorecon3 were run a few days ago under 5.2. Yesterday I installed
>> 5.3 and we ran the following:
>>
>> export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer
>> recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
>>
>> It ran for about 4.5 hours and then gave this error:
>>
>>
>> --
>> -
>> [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log
>> SUBJECTS_DIR/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer
>> FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4
>> Loading source label.
>> Invalid argument
>> ERROR reading
>> /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.
>> label
>> Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24
>> 19:32:05 EDT 2008 x86_64 x86_64 x86_64
>> GNU/Linux
>>
>> recon-all -s s_ALS51 exited with ERRORS at Mon Jun  3 18:32:01 EDT 2013
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>> --
>> -
>>
>> Some help would be appreciated. There is a file lh.BA1.label but not
>> lh.BA1.thresh.label, indeed there are no
>> files with "thresh" in their name under that subject.
>>
>> Thanks!
>>
>> -Robert
>>
>> **
>> Electronic Mail is not secure, may not be read every day, and should not
>> be used for urgent or sensitive issues
>>
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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>
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Re: [Freesurfer] error in 5.3

[Welsh, Robert]

ah, that probably got there from the 5.2 recon-all. I'll go in and
manually change those.

thanks

-robert


On 6/4/13 8:59 AM, "Bruce Fischl"  wrote:

Hi Robert

I think you need to symlink the fsaverage dir to the 5.3 fsaverage
instead of 5.2

cheers
Bruce
On Tue, 4 Jun 2013, Welsh, Robert wrote:

> Hi,
> 
> We were re-processing a subject to test the fix for 5.2 to 5.3. The
>initial recon-all and subsequent autrecon2
> and autorecon3 were run a few days ago under 5.2. Yesterday I installed
>5.3 and we ran the following:
> 
> export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer
> recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
> 
> It ran for about 4.5 hours and then gave this error:
> 
> 
>--
>-
> [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log
> SUBJECTS_DIR/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer
> FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4
> Loading source label.
> Invalid argument
> ERROR reading 
>/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.
>label
> Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24
>19:32:05 EDT 2008 x86_64 x86_64 x86_64
> GNU/Linux
> 
> recon-all -s s_ALS51 exited with ERRORS at Mon Jun  3 18:32:01 EDT 2013
> 
> To report a problem, see
>http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
>--
>-
> 
> Some help would be appreciated. There is a file lh.BA1.label but not
>lh.BA1.thresh.label, indeed there are no
> files with "thresh" in their name under that subject.
> 
> Thanks!
> 
> -Robert
> 
> **
> Electronic Mail is not secure, may not be read every day, and should not
>be used for urgent or sensitive issues
> 
> 
>


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[Freesurfer] error with trying 5.3 on 5.2 data for autorecon2 and autorecon3, balabel throwing error.

[Welsh, Robert]

Hi all,

In our efforts to take our 5.2 edits to 5.3 we tried the command below (in the 
attached thread), but we also tried the command

recon-all –s [subject-d] -autorecon2 –autorecon3

and those jobs are also running for some time but then crashing with the same 
error complaining that lh.BA1.thresh.label does not exist.

We are on RedHat 5.2, running the 2.6.18-19.1.13.e15 kernel and using the BASH 
environment.  We are using the release 5.3.0-centos04.

The log and other relevant files can be found at:

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.cmd

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.log

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.env

http://www-personal.umich.edu/~rcwelsh/bug/recon-all.error

I've dug into the code and see that the block of code in recon-all was 
introduced going from 5.2 to 5.3.

# generate .thresh labels
 foreach balabel (BA1 BA2 BA3a BA3b BA4a BA4p BA6 BA44 BA45 V1 V2 MT)
  set cmd=(mri_label2label \
--srcsubject fsaverage \
--srclabel 
$SUBJECTS_DIR/fsaverage/label/${hemi}.${balabel}.thresh.label \
--trgsubject $subjid \
--trglabel ./${hemi}.${balabel}.thresh.label \
--hemi ${hemi} \
--regmethod surface)
  echo "\n $cmd \n"|& tee -a $LF |& tee -a $CF
  if($RunIt) $fs_time $cmd |& tee -a $LF
  if($status) goto error_exit;
end # balabel

This is what is throwing the error.

Hopefully, we can get this resolved soon.

(Also as a side note in the version 5.2 we had to comment out the reference to 
perirhinal in the first "foreach balabel" loop as perirhinal was giving a bug)

Thanks,

-Robert

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Re: [Freesurfer] mri_glmfit-sim error

[Glen Lee]

Hi Doug,
I tried as you suggested, but i've got the following error:  e.g.,cannot
find any csd files.
However, I can see them stored in csd folder as shown below:

/2D/results/LH/GLM/csd> ls
mc-z.negative.j001-osgm.csd  perm.abs.2.j001-osgm.csd

I'm guessing that I need to define the path for this csd folder?

 Here is the command line that I typed in:
 mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim  --overwrite

 -Glen









On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve wrote:

>
> hi Glen, no cluster will show up if the p-value for all clusters is above
> .05. You can change this with --cwpvalthresh to something like .99. That
> should give you all the clusters. Also, you don't have to run the full
> simulation again; you can use the --no-sim option and it will use the
> simulation that you already did.
> doug
>
>
>
> On 6/3/13 9:45 PM, Glen Lee wrote:
>
> Indeed, I initially tried 10,000 iterations and got nothing.
> What else then could have gone wrong?
>
> FYI, I use v5.1.0.
>
>
>  On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> You will need more like 1 iterations instead of 100.
>> doug
>>
>> On 06/03/2013 04:49 PM, Glen Lee wrote:
>> > Hello Freesurfer experts--
>> >
>> > I ran mri_glmfit-sim to validate the group level GLM result (which was
>> > already done using mri_glmfit), but I was not able to get any result
>> > out of it.
>> >
>> >  Even with a quite liberal threshold (2), no vertices came out (below
>> > is what I typed in for the random permutation).
>> >
>> >  mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign
>> > abs --overwrite
>> >
>> > What is strange is that I was clearly see a number of clusters when I
>> > overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster
>> > shows up in  perm.abs.2.sig.cluster.mgh.
>> > I should be able to see the identical map between those right?
>> >
>> > FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below.
>> > As can be seen, nothing is listed in the stats table.
>> >
>> > Any of your help would be greatly appreciated.
>> > -Glen
>> >
>> >
>> >
>> >
>> >
>> >
>> > # Cluster Growing Summary (mri_surfcluster)
>> > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
>> > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
>> > # CreationTime 2013/06/03-20:19:31-GMT
>> > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
>> > GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
>> > GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
>> > GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
>> > GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
>> > GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
>> > GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
>> > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
>> > GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
>> > # cwd /glen/2D/results/LH
>> > # sysname  Linux
>>  > # hostname sumo.uphs.upenn.edu 
>>  > # machine  x86_64
>> > # FixVertexAreaFlag 1
>> > # FixSurfClusterArea 1
>> > #
>> > # Input  GLM/osgm/sig.mgh
>> > # Frame Number  0
>> > # srcsubj fsaverage_sym
>> > # hemi lh
>> > # surface white
>> > # annot aparc
>> > # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
>> > # SearchSpace_mm2 59961.4
>> > # SearchSpace_vtx 82070
>> > # Bonferroni 0
>> > # Minimum Threshold 2
>> > # Maximum Threshold infinity
>> > # Threshold Signabs
>> > # AdjustThreshWhenOneTail 1
>> > # CW PValue Threshold: 0.05
>> > # Area Threshold0 mm^2
>> > # CSD thresh  2.00
>> > # CSD nreps100
>> > # CSD simtype  perm
>> > # CSD contrast osgm
>> > # CSD confint  90.00
>> > # Overall max 3.495 at vertex 61659
>> > # Overall min -4.18843 at vertex 73402
>> > # NClusters  0
>> > # Total Cortical Surface Area 59961.4 (mm^2)
>> > # FixMNI = 0
>> > #
>> > # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ  CWP
>> >  CWPLowCWPHi   NVtxs   Annot
>> >
>> >
>>  > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>>
>>
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>> 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
>> HelpL

Re: [Freesurfer] mri_mc vs. recon-all surfaces

[Bruce Fischl]

Hi Oscar

what do you mean by "the CSF surface"? Outside the brain or in the 
ventricles? If outside, there is some code for creating boundary element 
models for EEG/MEG analysis.


There is no trivial way to create a single surface. The way I've done it in 
the past is to replace the lh or rh values in the filled.mgz with the other 
one and go from there, but it's not meant to work that way and you have to 
mess with it a fair amount.


cheers
Bruce


On Tue, 4 Jun 2013, Oscar Esteban 
wrote:



Dear all,
I need to extract three surfaces from MRI data:

- GM-WM interface -> thus, lh.white and rh.white would be the answer.
- Pial interface -> thus, lh.pial + rh.pial
- CSF surface

For CSF, as far as I know, the best option would be to generate a binary volume 
merging the appropriate labels
from aseg.mgz. Then use mri_mc to obtain the surface, right?

For white and pial I guess the best option would be to use the recon-all 
outcome, but I have two questions:
* Is there any mean to merge both hemispheres? I've tried several methods but I 
get trouble with the
consistency of the cells... the points are aggregated, but no work is done to 
merge cells and remove points.
* What are the differences between the recon-all outcome 
(lh.pial,rh.pial,lh.white,rh.white) with respect
obtaining masks from aseg.mgz and then mri_mc?

Thank you so much

Best regards,
Oscar Esteban


--
Oscar Esteban
PhD Student / Researcher

Biomedical Image Technologies (BIT), UPM
ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain)
+34 915 495 700 ext.4234

Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5
ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland

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Re: [Freesurfer] recon-all error

[Bruce Fischl]

Hi Rafa

that sounds like a bug. Can you gzip and upload the whole subject dir?

cheers
Bruce
On 
Tue, 4 Jun 2013, Rafa X wrote:



Dear freesurfer experts,

I was running an autorecon2 in the recon-all but always gives me this memory 
allocation error, only on this
subject. Im using FS v5.1



#@# ASeg Stats Mon Jun  3 20:13:11 CEST 2013
/root/trabajo/freesurfer/subjects/qsm1_17_stats2_g

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
--empty --excludeid 0 --excl-ctxgmwm
--supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --ctab 
/root/trabajo/freesurfer/ASegStatsLUT.txt --subject
qsm1_17_stats2_g


$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --excludeid 0
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name 
norm --in-intensity-units MR
--etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab 
/root/trabajo/freesurfer/ASegStatsLUT.txt --subject
qsm1_17_stats2_g
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user     root
atlas_icv (eTIV) = 1196346 mm^3    (det: 1.628380 )
Loading mri/aseg.mgz
Getting Cerebral WM volumes from surface
lh white matter volume 206011
rh white matter volume 198149
Getting Cerebral GM and WM volumes from surfaces
lh surface-based volumes (mm3): wTot = 235659.045132,  pTot = 416409.266434 c = 
180750.221302
rh surface-based volumes (mm3): wTot = 223785.748405,  pTot = 402494.420361 c = 
178708.671956
MRIalloc: could not allocate 540094766 frames

Computing SupraTentVolCor
Cannot allocate memory
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun  3 20:18:36 CEST 
2013

For more details, see the log file 
/root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Any help will be appreaciated,

Many thanks in advance
Rafa

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[Freesurfer] Parameterization Optseq

[Laura Dekkers]

Dear Dr Greve,

Together with Dr Hilde Huizenga I am implementing an fMRI study in which we
would like to optimize the design by using Optseq2.  We have a few
questions. Could you please help us out?
Our task consists of 3 runs of 72 trails each, in which participants are
presented with a fixation cross that remains on the screen for a fixed
duration of 1 sec, followed by one out of nine different stimuli that
remains on the screen for a fixed duration of 4 sec.
This gives a scan duration of 360 sec. We would then like to add 25%
jitter, which results in a scan duration of 450 sec, and as TR = 2.0, this
results in 225 time points.

However, Optseq yields an error if ntp is set to 225, ev duration set to
4.0, psdwin dPSD to 1.0 , tnullmin to 1.0 and tnullmax to 6.0
ERROR: could not enforce tNullMax=6 (ntries=10)
You will need to reduce the number of time points
or increase the number of presentations.

However, reducing the number of time points makes Optseq to only insert
null events of 1.0 or rarely 2.0 sec without much variation. Optimization
with ntp set to 225, ev duration set to 5.0 (=fixed duration of fix +
stimulus), psdwin dPSD to 1.0 , tnullmin to 0.0 (1.0 does not work) and
tnullmax to 6.0 does work. However, this renders Optseq to insert null
events of a fixed duration op 1.0 sec, which is not what we want.

Could you please advise us in how to set these parameters?

Thank you in advance.

Best regards,
Laura Dekkers

-- 
 Laura M.S. Dekkers, MSc
Research assistant
University of Amsterdam - Department of Developmental Psychology
Weesperplein 4
1018 XA Amsterdam - The Netherlands
E-mail: lmsdekk...@gmail.com
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Re: [Freesurfer] error in 5.3

[Bruce Fischl]

Hi Robert

I think you need to symlink the fsaverage dir to the 5.3 fsaverage 
instead of 5.2


cheers
Bruce
On Tue, 4 Jun 2013, Welsh, Robert wrote:


Hi,

We were re-processing a subject to test the fix for 5.2 to 5.3. The initial 
recon-all and subsequent autrecon2
and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and 
we ran the following:

export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer
recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3

It ran for about 4.5 hours and then gave this error:

---
[rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log
SUBJECTS_DIR    /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer
FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4
Loading source label.
Invalid argument
ERROR reading 
/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.label
Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 
EDT 2008 x86_64 x86_64 x86_64
GNU/Linux

recon-all -s s_ALS51 exited with ERRORS at Mon Jun  3 18:32:01 EDT 2013

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---

Some help would be appreciated. There is a file lh.BA1.label but not 
lh.BA1.thresh.label, indeed there are no
files with "thresh" in their name under that subject.

Thanks!

-Robert

**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues


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[Freesurfer] hippocampal subfield segmentation

[Claudia Dacquino]

Hi guys!
I have a dataset including hippocampal subfields obtained through the
-hippo-subfields flag. I want to have a measure of total hippo volume and
I'm not sure  which structures should I include in the sum. I was thinking
to exclude fimbria and fissure and sum the others. Am I right? Or should I
simply sum all the structures?
Any help is more than welcome
Cheers,
Fabrizio
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[Freesurfer] mri_mc vs. recon-all surfaces

[Oscar Esteban]

Dear all,

I need to extract three surfaces from MRI data:

- GM-WM interface -> thus, lh.white and rh.white would be the answer.
- Pial interface -> thus, lh.pial + rh.pial
- CSF surface

For CSF, as far as I know, the best option would be to generate a binary
volume merging the appropriate labels from aseg.mgz. Then use mri_mc to
obtain the surface, right?

For white and pial I guess the best option would be to use the recon-all
outcome, but I have two questions:
* Is there any mean to merge both hemispheres? I've tried several methods
but I get trouble with the consistency of the cells... the points are
aggregated, but no work is done to merge cells and remove points.
* What are the differences between the recon-all outcome
(lh.pial,rh.pial,lh.white,rh.white) with respect obtaining masks from
aseg.mgz and then mri_mc?

Thank you so much

Best regards,
Oscar Esteban


-- 
Oscar Esteban
PhD Student / Researcher

Biomedical Image Technologies (BIT), UPM
ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid
(Spain)
+34 915 495 700 ext.4234

Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5
ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland
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[Freesurfer] first level glm analysis on surface space

[Subhabrata Chaudhury]

Hello All,

I have run recon-all on some subjects. I have functional BOLD data on these 
subjects too. I am doing fmri preprocessing in spm. I have created register.dat 
by registering the meanBOLD image to the freesurfer reconstructed data. I am 
intending to do the following - 
I want to take each functional volume corresponding to each TR and move each 
volume to freesurfer and make a BOLD surface file in freesurfer (.mgh file). 
Then I want to run first level glm on the data like its done for volume data in 
spm, fsl, afni etc. 
My question is are there tools in freesurfer to do this on surfaces ? 
If not, can the mgh file be converted to a gifti file and maybe it can be used 
to make first level glms in afni, spm or fsl ?
I will really appreciate your opinion about this. 

Thank you very much,

Subha
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[Freesurfer] Surface area measurement method

[Andreas Berger]

Hello FreeSurfers,

after reading this [1] paper about measuring surface area, i realized i don't 
know what the default way of measuring surface area is in FreeSurfer. Is it 
similar to what's described in the paper? Could you point me to the right 
documentation or publication?
Forgive me if i've overlooked it, i found something for thickness, but not for 
area. To clarify, i don't mean parcellation-based areas, i mean the measure 
that i find in /surf/hemi.area.


thanks,
regards,
Andreas


[1] Measuring and comparing brain cortical surface area and other areal 
quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov P, 
Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43
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[Freesurfer] Postdoctoral Fellow - University of Oslo

[Lars Tjelta Westlye]

A three-year term position as Postdoctoral Fellow (governmental 
position code 1352) is available at the Norwegian Centre for Mental 
Disorders Research (NORMENT) and the KG Jebsen Centre for Psychosis 
Research – TOP Study Group, Institute of Clinical Medicine, University 
of Oslo and Oslo University Hospital, Norway.

http://uio.easycruit.com/vacancy/983405/70331?iso=no

** Job Description

NORMENT coordinates a translational multicenter study involving all 
psychiatric hospital departments in Oslo and several research groups at 
the University of Oslo. The main purpose of the research is to 
disentangle and characterize the neurobiological, genetic, psychological 
and environmental factors contributing to the development of severe 
mental disorders. Through our extensive infrastructure for clinical 
evaluations, neuropsychological testing, MRI brain imaging and 
biobanking we are assembling a comprehensive database comprising genetic 
and brain imaging data from a large number of healthy controls and 
patients suffering from psychotic disorders including schizophrenia and 
bipolar disorders. The postdoctoral fellow will play a central role in 
the analysis and dissemination of data from this large imaging genetics 
database. The research will be carried out as part of a 
cross-disciplinary team of researchers in the Multimodal Imaging and 
Biostatistics groups at NORMENT in close collaboration with researchers 
at the University of California San Diego and deCODE Genetics.

** We offer

An ambitious and exciting research environment with a strong 
multidisciplinary profile and excellent opportunities for academic 
development at NORMENT, which was recently granted Centre of Excellence 
Status by the Research Council of Norway. A postdoctoral position in 
Norway is equivalent to the US position of assistant professor and is 
intended to prepare and qualify talented candidates for a research 
career.

Salary is in the range between ltr 57 and ltr 65, i.e. from NOK 473 400 
to NOK 548 700, depending on qualifications.

Pension and national health insurance is included in addition to 
several attractive welfare arrangements 
(http://www.uio.no/english/for-employees/employment/welfare).

** Qualifications

The ideal candidate is ambitious and highly motivated for pursuing a 
career in science, hold a PhD in neuroimaging, computational 
neuroscience, biomedical engineering, cognitive neuroscience, or 
equivalent, have a strong background and interest in neuroscience, MRI 
analysis and statistics, and an excellent publication record. Candidates 
with a strong interest in and experience with methods for integrating 
multimodal imaging measures, including structural MRI, diffusion tensor 
imaging (DTI), and functional MRI, are in particular encouraged to 
apply. Experience with imaging genetics is an advantage.

** The application

Applications are submitted through the University online recruitment 
system and must include application letter including motivation for 
applying for the position, CV summarizing education, relevant work 
experience, grants etc, a complete list of publications and academic 
work, and contact details of 2-3 references. Application deadline: June 
30 2013.

After the initial screening process, short-listed candidates may be 
asked to submit selected publications, educational certificates and 
transcripts of records. Interviews may be included as part of the 
selection process.

For any informal enquiries regarding the position, please contact 
professor Ole A. Andreassen (o.a.andreas...@medisin.uio.no) and 
associate professor Lars T. Westlye (l.t.west...@psykologi.uio.no).

http://uio.easycruit.com/vacancy/983405/70331?iso=no
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[Freesurfer] recon-all error

[Rafa X]

Dear freesurfer experts,

I was running an autorecon2 in the recon-all but always gives me this
memory allocation error, only on this subject. Im using FS v5.1



#@# ASeg Stats Mon Jun  3 20:13:11 CEST 2013
/root/trabajo/freesurfer/subjects/qsm1_17_stats2_g

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz
--empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in
mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --ctab
/root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g


$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray
--in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --ctab
/root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user root
atlas_icv (eTIV) = 1196346 mm^3(det: 1.628380 )
Loading mri/aseg.mgz
Getting Cerebral WM volumes from surface
lh white matter volume 206011
rh white matter volume 198149
Getting Cerebral GM and WM volumes from surfaces
lh surface-based volumes (mm3): wTot = 235659.045132,  pTot = 416409.266434
c = 180750.221302
rh surface-based volumes (mm3): wTot = 223785.748405,  pTot = 402494.420361
c = 178708.671956
MRIalloc: could not allocate 540094766 frames

Computing SupraTentVolCor
Cannot allocate memory
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT
2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun  3 20:18:36
CEST 2013

For more details, see the log file
/root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Any help will be appreaciated,

Many thanks in advance
Rafa
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