date:20130509

Hi Jon

yes, the subject and hemi need to be defined (they are required 
parameters)
Bruce
On Wed, 8 May 2013, Jonathan Holt wrote:

 Hi all,
 combed through the mail archives to figure out how to work with multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 
 mris_make_surfaces -dura memprage_echo%d.mgz 
 
 do the subjid and hemispheres need to be specified as per the 1st line?
 
 jon
 
 
 
 

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Re: [Freesurfer] Working with MEMPRAGE

Thanks Bruce,

should the hemisphere's be processed separately, or how do I signify lh and rh 
simultaneously? 

Also, should the fact that after running mris_make_surfaces, it says detecting 
dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different 
echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly.

jon
On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:

 Hi Jon
 
 yes, the subject and hemi need to be defined (they are required parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:
 
 Hi all,
 combed through the mail archives to figure out how to work with multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres 
 need to be specified as per the 1st line?
 jon
 
 
 
 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] Qdec error and design problem

Hi Sinead, you cannot use QDEC for this design since it has one factor 
with 3 levels (only 2 levels possible now). You can create an FSGD file, 
follow the example here:

http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V

doug


On 05/09/2013 06:42 AM, Sinead Kelly wrote:
 Dear all,

 I am trying to run statistical analysis on cortical thickness data 
 using Qdec. I have one group of control subjects that are split into 
 three genotype groups. I want to investigate if cortical thickness 
 significantly between the three genotype groups. Is it possible to 
 look at differences between three groups using Qdec? I am getting the 
 following error when I try to analyse - ERROR: QdecGlmDesign::Create: 
 zero factors!

 I would really appreciate if anyone could shed some light on this for 
 me as this is the first time I have used Qdec and I don't know what is 
 causing this error.

 Thank you for your help.

 Sinead

 -- 
 Sinead Kelly
 Neuropsychiatric Genetics Group
 Trinity Centre
 St. James's Hospital
 Dublin 8


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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Working with MEMPRAGE

can you send me the full command line? It should say 4 echoes, not 0
On Thu, 
9 May 2013, Jonathan Holt wrote:

 Thanks Bruce,

 should the hemisphere's be processed separately, or how do I signify lh and 
 rh simultaneously?

 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've 
 got 4 different echos, all mgzs in the directory. I have a feeling I'm doing 
 this incorrectly.

 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:

 Hi Jon

 yes, the subject and hemi need to be defined (they are required parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:

 Hi all,
 combed through the mail archives to figure out how to work with multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres 
 need to be specified as per the 1st line?
 jon



 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] Labels and parcellations

On 05/08/2013 05:24 PM, Tudor Popescu wrote:
Sorry, one more iteration:

1) Command mri_annotation2label --subject 01 --hemi lh --aparc.a2009s
--outdir $SUBJECTS_DIR/01/myLabelsDestrieux doesn't recognise the
aparc.2009s flag (I tried a few other variations with no luck)!
The syntax is --annot aparc.2009s
If you run mri_annotation2label with --help it will tell you the syntax.

1') Assuming the above command works and I get .label files
corresponding to all Destrieux structures, what is the exact call to
mri_glmfit that will do the two contrasts I mentioned (group
comparison of CT, and comparison of CT-behaviour correlation)?

1'') How should the design matrix contrast files (arguments for
calling mri_glmfit) be created, for these analyses?
Have you looked at our group analysis tutorials?

2) ..so when would I use a mask, in a ROI analysis, as opposed to a label?
Functionally, there is no difference. If you had a process that
generated a mask, then you would just use that. You can convert any mask
to a label with mri_cor2label. mri_glmfit will give you the same result.

3) I'm still not sure as to the answer to my question: regardless of
what space I do it in, does it pay off to create the label/mask that
Ill use in the ROI analysis /manually /for each individual subject
(i.e. taking into account individual anatomy), as opposed to just
taking it from an atlas and using /the same /label/mask with /all
/subjects?
If you are using it as a mask for voxel-wise analysis, then you need a
mask in the common space. You could get this mask by drawing the mask in
the common space. Or you could draw the mask on each individual, then
map the masks to the common space. But you would need to then merge all
those masks together into a single binary mask. I don't know whether one
would be better than the other, but the individual masks will surely be
a lot more work.

4) Bingo - this creates an image as I wanted, but now the mouse cursor
no longer tells me the structure above which I hover the mouse (so a
legend to each color, much like in Fig 1 of the Desikan paper)
I don't understand what you mean here. The name of the structure should
appear in the control window. It does not appear in the image window
like in Fig 1.
doug

I really appreciate your patience Doug, thanks :)
Tudor

On 8 May 2013 18:56, Douglas N Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:

On 05/08/2013 01:28 PM, Tudor Popescu wrote:

2) ..and when would you use a surface mask versus a
surface label?

It is just a matter of convenience.

Sorry, I meant I don't really understand what the difference
is between a label and a mask, and in which circumstances each
should be used. I tried finding an answer on the wiki but no
luck..

A label is a text file with a list of points in the label. A mask
is binary file (eg, mgh or nii) with 1s where the mask is and 0s
otherwise.

3) (it seems you skipped over this one:) )

Sorry:) what are you going to do with the ROI?

Use it mri_glmfit, in order to compare cortical thickness in
that ROI between groups, and also (in a different design) to
compare the correlations between thickness and a behavioural
predictor

If you're doing the final analysis in the group space, then just
use the ROI in the group space.

4) This opens up a coronal slice rather than a 3D
image as in
the picture I linked to. Do I need to do anything else in
tkmedit after it opens? (I tried pressing some
buttons, and
some menu options, with no luck)

that was generated with tksurfer, something like tksurfer
subject
lh pial -aparc

Using that command, I get a brain
http://www.4shared.com/photo/sRcnX93M/8-05-2013_18-25-04.html that
has only little of its surface coloured, unlike the image

http://brainybehavior.com/neuroimaging/wp-content/uploads/2010/05/jt_rh_pial_freesurfer_tksurfer.png
that I linked to, in which it seems each major structure is
identified in its own colour, and these colours fill up the
entire brain (there's no grey surface left)

Change the annotation mode to be filled instead of outline mode.
In the tksurfer control window, it is the 4th button from the
right on the top row. It will say Draw Filled Labels when you
put the mouse over it

On 8 May 2013 16:54, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] Working with MEMPRAGE

I input:

mris_make_surfaces -dura memprage_echo%d.mgz subjid lh

it returns:

detecting dura using 0 echos from memprage_echo%d.mgz


Should I execute the command in the same directory as the mgz's? Should they be 
set up or placed in a specific directory? I also, as with recon-all, exported 
the proper subject directory beforehand. 


On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:

 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify lh and 
 rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've 
 got 4 different echos, all mgzs in the directory. I have a feeling I'm doing 
 this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
 Hi Jon
 
 yes, the subject and hemi need to be defined (they are required parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:
 
 Hi all,
 combed through the mail archives to figure out how to work with multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres 
 need to be specified as per the 1st line?
 jon
 
 
 
 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 


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Re: [Freesurfer] Working with MEMPRAGE

it needs to be:

mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh

note the 4 which tells it how many echoes to read

On Thu, 9 May 2013, Jonathan Holt wrote:

 I input:

 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh

 it returns:

 detecting dura using 0 echos from memprage_echo%d.mgz


 Should I execute the command in the same directory as the mgz's? Should they 
 be set up or placed in a specific directory? I also, as with recon-all, 
 exported the proper subject directory beforehand.


 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:

 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:

 Thanks Bruce,

 should the hemisphere's be processed separately, or how do I signify lh and 
 rh simultaneously?

 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've 
 got 4 different echos, all mgzs in the directory. I have a feeling I'm 
 doing this incorrectly.

 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:

 Hi Jon

 yes, the subject and hemi need to be defined (they are required parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:

 Hi all,
 combed through the mail archives to figure out how to work with multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon



 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] Using FSL matrix for Talairach transform

yep, can you upload the relevant datato our file drop?

On 05/09/2013 05:52 AM, Johannes Klein wrote:
 Hi Doug,
 Thanks! I've tried that now, but it didn't help. Looking at the output, I get 
 the impression that some of the axes might be swapped over. I've done a 
 manual registration now to process my subject.
 Maybe it's worth following this up for future use of FSL-supplied matrices - 
 however, the problem only applies to XFM-style output, and e.g. mri_vol2vol 
 works fine, so I guess there aren't many other users affected. If you like, I 
 can send you a few volumes and the associated registration matrix.
 Thanks for your help!
 Cheers,
 Johannes

 Douglas N Greve Wed, 08 May 2013 12:16:36 -0700

 Hi Johannes, as a quick fix can you try inverting the matrix?
 doug

 On 05/08/2013 01:31 PM, Johannes Klein wrote:
 Hi Doug,
 Thanks for your reply! I'm getting closer to a solution now, with
 tkregister2's display showing a correctly transformed mni305 file,
 but I still cannot get a valid talairach.xfm file out of this.

 Here's what I tried:
 tkregister2 --mov  /usr/local/freesurfer/average/mni305.cor.mgz
   --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg
 works fine.

 Next, to obtain a suitable .xfm file, I ran
 tkregister2 --mov  /usr/local/freesurfer/average/mni305.cor.mgz
   --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg  --xfmout
 testtal.xfm --noedit
 and copied the output (testtal.xfm) into mri/transforms/talairach.xfm

 Now, when I view the result with
 tkregister2 --s test --fstal --mgz
 the transform is way off again. Apparently, tkregister2 reads and
 interprets the FSL matrix correctly, but the output transform that I
 get is not in the right format for transforms/talairach.xfm.
 I wonder if I'm using the wrong output switch now - but looking at
 tkregister2's documentation, it seems to be the one to use?
 Thanks,
 Johannes



 Date: Tue, 07 May 2013 14:11:27 -0400
 From: Douglas N Greve gr...@nmr.mgh.harvard.edu
 
 mailto:gr...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform
 To: freesurfer@nmr.mgh.harvard.edu 
 mailto:freesurfer@nmr.mgh.harvard.edu
 Message-ID: 518943cf.7050...@nmr.mgh.harvard.edu
 
 mailto:518943cf.7050...@nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed

 Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure
 what regdat2xfm is doing.
 doug

 On 05/07/2013 12:42 PM, Johannes Klein wrote:
 Dear all,
 I have some tricky subjects that I cannot get to register properly
 with the standard Talairach process, or even the use-mritotal option.
 However, with some fiddling, I've produced a reasonable registration
 matrix with FSL's FLIRT.

 I'm now looking to convert my FSL registration matrix, and use it as
 Freesurfer's Talairach transform. From the documentation, I gathered
 that I need to get it into Freesurfer's xfm format, and I suppose
 this is a two step process.

 I converted the FLIRT-provided matrix cor2raw.xfm like so:
 tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz
   --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat

 I then converted register.dat to the xfm data format:
 regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz
 register.dat tal.xfm

 and finally replaced talairach.xfm in the transforms directory with
 the output of the last command. Unfortunately, this doesn't work, and
 the transform is very much off target when I view it in tkregister2.
 Obviously, I've made a mistake when converting between the different
 transforms - could anybody point me in the right direction?
 Thanks all,
 Johannes



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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu 
 mailto: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
 
 http://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 mailing list
 Freesurfer@nmr.mgh.harvard.edu

 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Working with MEMPRAGE

That was my suspicion, I've got them in the wrong folder. None of them are 
'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
nothing else.

Also the exact error has it looking in 
/example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz 

as opposed to /example/directory/subjects/subjid/mri/filled.mgz

I can rename subject directory if need be.


On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:

 is your SUBJECTS_DIR set properly? You need to put the memprage echoes in 
 the subject's mri dir
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Oh, simple mistake!
 
 However, now it spit's an error saying I need filled.mgz?
 
 
 On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
 
 it needs to be:
 
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
 
 note the 4 which tells it how many echoes to read
 
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 I input:
 
 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
 
 it returns:
 
 detecting dura using 0 echos from memprage_echo%d.mgz
 
 
 Should I execute the command in the same directory as the mgz's? Should 
 they be set up or placed in a specific directory? I also, as with 
 recon-all, exported the proper subject directory beforehand.
 
 
 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
 
 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify lh 
 and rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? 
 I've got 4 different echos, all mgzs in the directory. I have a feeling 
 I'm doing this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
 Hi Jon
 
 yes, the subject and hemi need to be defined (they are required 
 parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:
 
 Hi all,
 combed through the mail archives to figure out how to work with multi 
 echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon
 
 
 
 The information in this e-mail is intended only for the person to whom 
 it is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you 
 in error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 
 
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Working with MEMPRAGE

Did you run recon-all? It will create filled.mgz in the subject/mri dir



On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu wrote:

 That was my suspicion, I've got them in the wrong folder. None of them are 
 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
 nothing else.
 
 Also the exact error has it looking in 
 /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz 
 
 as opposed to /example/directory/subjects/subjid/mri/filled.mgz
 
 I can rename subject directory if need be.
 
 
 On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
 
 is your SUBJECTS_DIR set properly? You need to put the memprage echoes in 
 the subject's mri dir
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Oh, simple mistake!
 
 However, now it spit's an error saying I need filled.mgz?
 
 
 On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
 
 it needs to be:
 
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
 
 note the 4 which tells it how many echoes to read
 
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 I input:
 
 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
 
 it returns:
 
 detecting dura using 0 echos from memprage_echo%d.mgz
 
 
 Should I execute the command in the same directory as the mgz's? Should 
 they be set up or placed in a specific directory? I also, as with 
 recon-all, exported the proper subject directory beforehand.
 
 
 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
 
 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify lh 
 and rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? 
 I've got 4 different echos, all mgzs in the directory. I have a feeling 
 I'm doing this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
 Hi Jon
 
 yes, the subject and hemi need to be defined (they are required 
 parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:
 
 Hi all,
 combed through the mail archives to figure out how to work with multi 
 echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon
 
 
 
 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
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Re: [Freesurfer] recon-all completes without all the info..

2013-05-09 Thread Sudhin A. Shah

Hi! I am running this on ~26 datasets and some have exited with errors and 
others have not completed (~ 2 days).

Sorry, but what should I be running to get the following files?

1) T1.mgz
2) wm.mgz
3) aparc+aseg.mgz
4) brainmask.mgz
5) ribbon.mgz
6) And I need to run reg-feat2anat

I am quite certain that what I ran (successfully) before 

was recon-all -s xyx -i xyz -autorecon1 but when I ran this recently, all the 
files above did not populate.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Louis Nicholas Vinke 
[vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 07, 2013 12:05 PM
To: Sudhin A. Shah
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all completes without all the info..

Yes, the -all flag will run autorecon1, autorecon2, and autorecon3.

recon-all -all -i path to dicom/nii/mgz T1 image -s subjID

For that uncompleted subject you have though if sounds like you just need
to run autorecon2 and 3

recon-all -autorecon2 -autorecon3 -s subjID

On Tue, 7 May 2013, Sudhin A. Shah wrote:

 Is there 1 command line? I used to just run the 1 line.



 On May 7, 2013, at 10:19 AM, Louis Nicholas Vinke 
 vi...@nmr.mgh.harvard.edu wrote:

 Hi Sudhin,
 You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces 
 and all the cortical/sub-cortical measures.
 -Louis

 On Tue, 7 May 2013, Sudhin A. Shah wrote:

 On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote:

  Hi, This is a new issue as it used to run well before.. I run
  recon-all ... ... -autorecon1 - force and it completes without
  error but I don't have all the files..

  Attached is a screenshot. On the right is the output from a file
  that worked before and on the left is a newer folder..
 Screenshot.png___
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 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
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Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?


Does the cortex label have any holes in it and do the holes in your 
output correspond? Try it with out the --cortex flag.
doug

ps. Please remember to send to the list and not to me directly. That way 
others can benefit from the exchange and the record goes into our mail 
archive.



On 05/09/2013 11:07 AM, Glen Lee wrote:
 Hi Doug

 See below for the command line that I used.

 smoothK=4;

 mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ...
 num2str(smoothK) ' --cortex --sval ' 
 Functional_dir Subj '/GLM/all_base-sym_R.mgh '...




 On Wed, May 8, 2013 at 11:31 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Hi Glen, can you give us more information about what you did? Eg,
 command line?
 doug



 On 5/8/13 8:53 PM, Glen Lee wrote:
 Hello freesurfer experts,

 I'm a newbie for freesurfer and would like to ask a naive question.

 I've just applied smoothing onto a single surface mgh file using
 mri_surf2surf (with fwhm ==4) and examined the values in the
 output map.

 As it turns out, values become 0 in a number of vertices after
 smoothing while those in many other vertices look normal (i.e.,
 more or less similar to the values in the vertex of unsmoothed map).
 I'm not sure why this happened as smoothing average values
 locally within the kernel (4mm).

 Any helpful answers would be greatly appreciated.

 Glen

 p.s) fyi, the original EPI is a slap data covering only the
 temporal  occipital cortex.








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 The information in this e-mail is intended only for the person to
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 addressed. If you believe this e-mail was sent to you in error and
 the e-mail
 contains patient information, please contact the Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to
 you in error
 but does not contain patient information, please contact the
 sender and properly
 dispose of the e-mail.



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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

2013-05-09 Thread Nicola Toschi

Thanks Nick,

well that did change something... here is what i get now with any fs 
command:

/bin/tcsh: /lib64/libfreebl3.so: version `NSSRAWHASH_3.12.3' not found 
(required by /work2/rootbackup/usr/local/freesurfer/lib/libcrypt.so.1)

Should I update/substitute /lib64/libfreebl3.so al well?

thanks a lot,

Nicola

PS when running ldd ./mri_convert inside the bin dir, I get

not a dynamic executable



On 05/09/2013 06:02 AM, Nick Schmansky wrote:
 Nicola and Nick,

 Hi, its Nick (the other Nick :)). This looks like a new issue we haven't
 seen before that is specific to opensuse.  Can you try downloading the
 file libcrypt.so.1 from this location:

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/

 copy it to your freesurfer/lib dir, then set a lib path prior to
 setting-up (sourcing) freesurfer, like this:

 setenv FREESURFER_HOME whereever you installed freesurfer
 setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib
 source $FREESURFER_HOME/SetUpFreeSurfer.csh

 this libcrypt lib is from centos6, and i'm thinking that possibly opensuse
 implements crypt differently (working theory anyway).

 you can confirm that mri_convert is using this new lib by typing:

 cd $FREESURFER_HOME/bin
 ldd ./mri_convert

 and you should see libcrypt in the list with a path to the freesurfer/lib
 dir.

 Nick


 Hi Nick (Schmansky),

 sorry to jump back in on this thread - I have exactly the same issue
 (license file not valid) on the same OS (and not on others) with *all*
 fs commands. I have tried multiple license files from other working
 installations.

 Is there anything else i can try?

 Thanks a lot

 nicola

 On 5/8/2013 3:09 PM, Nick Schmansky wrote:
 Nick

 Can you email me the .license file that is being used?

 Thanks,

 N.


 On Wed, 2013-05-08 at 13:21 -0500, Nick Jones wrote:
 Hi Nick,

 Truncated the email.  I'm getting a license error for both the
 mri_convert command and the tkmedit command that you provided.  The
 original also yields a license error (no segfault).  You are right, my
 earlier test called tkmedit.bin directly.

 Thanks

 Nick

 On 05/08/2013 12:07 PM, Nick Schmansky wrote:
 Nick,

 Hi, I found what might the source of the problem and posted new
 versions
 of mri_convert and tkmedit.bin to this directory:

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/

 before trying the new mri_convert though, can you try the following?

 cd some writable directory
 mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz

 I'm guessing it will segfault or print the license problem.

 Now copy the new mri_convert (from the ftp link above) to the
 freesurfer/bin directory and try again.  It should work.  You can then
 also try the new tkmedit.bin.  Remember to copy the tkmedit.bin to the
 freesurfer/tktools directory and leave freesurfer/bin/tkmedit
 untouched
 (its a wrapper-script that sets-up paths to the tcl/tk/tix/blt libs,
 so
 tkmedit.bin cannot be run directly)

 Thanks,

 Nick





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 contains patient information, please contact the Partners Compliance
 HelpLine at
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Re: [Freesurfer] Working with MEMPRAGE

No, 

I believe my PI simply ran mri_convert on the 4 nii's, 

Clearly there is a better approach?

jon
On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:

 Did you run recon-all? It will create filled.mgz in the subject/mri dir
 
 
 
 On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu wrote:
 
 That was my suspicion, I've got them in the wrong folder. None of them are 
 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
 nothing else.
 
 Also the exact error has it looking in 
 /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz 
 
 as opposed to /example/directory/subjects/subjid/mri/filled.mgz
 
 I can rename subject directory if need be.
 
 
 On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
 
 is your SUBJECTS_DIR set properly? You need to put the memprage echoes in 
 the subject's mri dir
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Oh, simple mistake!
 
 However, now it spit's an error saying I need filled.mgz?
 
 
 On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
 
 it needs to be:
 
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
 
 note the 4 which tells it how many echoes to read
 
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 I input:
 
 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
 
 it returns:
 
 detecting dura using 0 echos from memprage_echo%d.mgz
 
 
 Should I execute the command in the same directory as the mgz's? Should 
 they be set up or placed in a specific directory? I also, as with 
 recon-all, exported the proper subject directory beforehand.
 
 
 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
 
 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify 
 lh and rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? 
 I've got 4 different echos, all mgzs in the directory. I have a 
 feeling I'm doing this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
 Hi Jon
 
 yes, the subject and hemi need to be defined (they are required 
 parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:
 
 Hi all,
 combed through the mail archives to figure out how to work with 
 multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon
 
 
 
 The information in this e-mail is intended only for the person to 
 whom it is
 addressed. If you believe this e-mail was sent to you in error and 
 the e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to 
 you in error
 but does not contain patient information, please contact the sender 
 and properly
 dispose of the e-mail.
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 
 
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
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 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] recon-all completes without all the info..

2013-05-09 Thread Louis Nicholas Vinke

Hi Sudhin,
You will need to add -autorecon2 and -autorecon3 to the command you ran 
before, or just replace all -autorecon# flags with the -all flag.

for new subjects:

recon-all -s xyx -i xyz -autorecon1 -autorecon2 -autorecon3

for subjects who already have completed autorecon1:

recon-all -s xyx -autorecon2 -autorecon3

The T1 and brainmask volumes should already exist after completing 
autorecon1.  The rest of those files are creating during autorecon2 and 
autorecon3.
-Louis

On Thu, 9 May 2013, Sudhin A. Shah wrote:

 Hi! I am running this on ~26 datasets and some have exited with errors and 
 others have not completed (~ 2 days).

 Sorry, but what should I be running to get the following files?

 1) T1.mgz
 2) wm.mgz
 3) aparc+aseg.mgz
 4) brainmask.mgz
 5) ribbon.mgz
 6) And I need to run reg-feat2anat

 I am quite certain that what I ran (successfully) before

 was recon-all -s xyx -i xyz -autorecon1 but when I ran this recently, all the 
 files above did not populate.


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Louis Nicholas Vinke 
 [vi...@nmr.mgh.harvard.edu]
 Sent: Tuesday, May 07, 2013 12:05 PM
 To: Sudhin A. Shah
 Cc: Freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] recon-all completes without all the info..

 Yes, the -all flag will run autorecon1, autorecon2, and autorecon3.

 recon-all -all -i path to dicom/nii/mgz T1 image -s subjID

 For that uncompleted subject you have though if sounds like you just need
 to run autorecon2 and 3

 recon-all -autorecon2 -autorecon3 -s subjID

 On Tue, 7 May 2013, Sudhin A. Shah wrote:

 Is there 1 command line? I used to just run the 1 line.



 On May 7, 2013, at 10:19 AM, Louis Nicholas Vinke 
 vi...@nmr.mgh.harvard.edu wrote:

 Hi Sudhin,
 You'll need to also run -autorecon2 and -autorecon3 in order to get 
 surfaces and all the cortical/sub-cortical measures.
 -Louis

 On Tue, 7 May 2013, Sudhin A. Shah wrote:

 On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote:

  Hi, This is a new issue as it used to run well before.. I run
  recon-all ... ... -autorecon1 - force and it completes without
  error but I don't have all the files..

  Attached is a screenshot. On the right is the output from a file
  that worked before and on the left is a newer folder..
 Screenshot.png___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.



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Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?

2013-05-09 Thread Glen Lee

Thanks Doug.
I'll give it a try right away.

Glen

On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

Does the cortex label have any holes in it and do the holes in your output
correspond? Try it with out the --cortex flag.
doug

ps. Please remember to send to the list and not to me directly. That way
others can benefit from the exchange and the record goes into our mail
archive.

On 05/09/2013 11:07 AM, Glen Lee wrote:

Hi Doug

See below for the command line that I used.

smoothK=4;

mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ...
num2str(smoothK) ' --cortex --sval ' Functional_dir
Subj '/GLM/all_base-sym_R.mgh '...

On Wed, May 8, 2013 at 11:31 PM, Douglas Greve
gr...@nmr.mgh.harvard.edumailto:
gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote:

Hi Glen, can you give us more information about what you did? Eg,
command line?
doug

On 5/8/13 8:53 PM, Glen Lee wrote:

Hello freesurfer experts,

I'm a newbie for freesurfer and would like to ask a naive question.

I've just applied smoothing onto a single surface mgh file using
mri_surf2surf (with fwhm ==4) and examined the values in the
output map.

As it turns out, values become 0 in a number of vertices after
smoothing while those in many other vertices look normal (i.e.,
more or less similar to the values in the vertex of unsmoothed map).
I'm not sure why this happened as smoothing average values
locally within the kernel (4mm).

Any helpful answers would be greatly appreciated.

Glen

p.s) fyi, the original EPI is a slap data covering only the
temporal occipital cortex.

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If the e-mail was sent to
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but does not contain patient information, please contact the
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dispose of the e-mail.

--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs:
surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
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Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Working with MEMPRAGE

Hi Jon

you need to run recon-all all the way through, then run the command I sent 
you with the echoes in the mri dir

cheers
Bruce
On Thu, 9 May 2013, Jonathan Holt wrote:

 No,

 I believe my PI simply ran mri_convert on the 4 nii's,

 Clearly there is a better approach?

 jon
 On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:

 Did you run recon-all? It will create filled.mgz in the subject/mri dir



 On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu wrote:

 That was my suspicion, I've got them in the wrong folder. None of them are 
 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
 nothing else.

 Also the exact error has it looking in 
 /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz

 as opposed to /example/directory/subjects/subjid/mri/filled.mgz

 I can rename subject directory if need be.


 On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:

 is your SUBJECTS_DIR set properly? You need to put the memprage echoes in
 the subject's mri dir
 On Thu, 9 May 2013, Jonathan Holt wrote:

 Oh, simple mistake!

 However, now it spit's an error saying I need filled.mgz?


 On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:

 it needs to be:

 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh

 note the 4 which tells it how many echoes to read

 On Thu, 9 May 2013, Jonathan Holt wrote:

 I input:

 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh

 it returns:

 detecting dura using 0 echos from memprage_echo%d.mgz


 Should I execute the command in the same directory as the mgz's? Should 
 they be set up or placed in a specific directory? I also, as with 
 recon-all, exported the proper subject directory beforehand.


 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:

 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:

 Thanks Bruce,

 should the hemisphere's be processed separately, or how do I signify 
 lh and rh simultaneously?

 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? 
 I've got 4 different echos, all mgzs in the directory. I have a 
 feeling I'm doing this incorrectly.

 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:

 Hi Jon

 yes, the subject and hemi need to be defined (they are required 
 parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:

 Hi all,
 combed through the mail archives to figure out how to work with 
 multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon



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Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?

2013-05-09 Thread Glen Lee

You are right, Doug.
The number of zero-value vertices got reduced more and more when I
increased the smoothing kernel size.

Thanks a lot for your help!
-Glen

On Thu, May 9, 2013 at 3:29 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

command looks ok. Just using a slab would create 0s in a lot of places,
but those 0s should get smoothed with other non 0s

On 05/09/2013 02:06 PM, Glen Lee wrote:

On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
wrote:

Does the cortex label have any holes in it and do the holes in
your output correspond? Try it with out the --cortex flag.
doug
- there was some improvement when I did smoothing after removed
'-- cortex flag', such that the number of vertex with '0' was
decreased from 35785 to 21898.

I piped in a slab EPI image (covering only temporal regions) to the
freesurfer using mri_vol2surf function (see below for more details).
I'm guessing this has caused some holes (i.e., zero-value vertices) in
labels during 2D reconstruction?
Or alternatively, do you see any problem in the command below?

mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold'
num2str(run) zero_digit num2str(TR) '.nii' ...
' --srcreg ~/DMPC/3D/data/' Subj
'/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o
~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR)
'_R.mgh'];

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

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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Kayle Sawyer

Hi all,

Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using 
the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead 
specify the multiecho scans for recon-all, do we need to give any additional 
parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect 
dura and refine pial surfaces in mris_make_surfaces, as described below? Or 
would we have to run recon-all with the RMS, then after it finishes re-run 
mris_make_surfaces manually with the -dura flag to refine the pial surface?

Also, I'd like to make sure we are using dcmunpack properly. We take the 
scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run 
number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, 
and the RMS gets put into a separate mgz file.

Thanks,
-Kayle

On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
 Message: 35
 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT)
 From: Bruce Fischl fis...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Working with MEMPRAGE
 To: Jonathan Holt whats...@umich.edu
 Cc: freesurfer@nmr.mgh.harvard.edu
 Message-ID:
   alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu
 Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
 
 it needs to be:
 
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
 
 note the 4 which tells it how many echoes to read
 
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 I input:
 
 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
 
 it returns:
 
 detecting dura using 0 echos from memprage_echo%d.mgz
 
 
 Should I execute the command in the same directory as the mgz's? Should they 
 be set up or placed in a specific directory? I also, as with recon-all, 
 exported the proper subject directory beforehand.
 
 
 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
 
 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify lh 
 and rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've 
 got 4 different echos, all mgzs in the directory. I have a feeling I'm 
 doing this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
 Hi Jon
 
 yes, the subject and hemi need to be defined (they are required 
 parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:
 
 Hi all,
 combed through the mail archives to figure out how to work with multi 
 echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon
 


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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] Working with MEMPRAGE