Re: [Freesurfer] Freeview colorbar with command line & white background?

[Xiuming Zhang (Ming)]

Hi Ruopeng,

Thanks a lot for helping clarify this!

May I ask a follow-up question? Why am I getting a symmetric-around-0 colorbar 
(please see the attachment)? I only have values from 3.99e-6 to 1.2e-5.



Thank you very much!

Best regards,
Xiuming (Ming)___
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] average values per cluster

[maaike rive]

Ok, thanks!
Maaike

> Op 6 feb. 2015 om 17:49 heeft "Douglas N Greve"  
> het volgende geschreven:
> 
> 
> There is not a way to build more flexible models in the FSGD structure. 
> However, you can create your own design matrix and include anything you 
> want in it and pass it to mri_glmfit with --X instead of --fsgd.
> 
> doug
> 
>> On 02/05/2015 06:13 AM, maaike rive wrote:
>> 
>> Hi Doug,
>> 
>> I hope I'm not driving you crazy, but I have some additional questions 
>> regardig the DOSS/DODS models. Also because of the SPSS discrepancies.
>> 
>> First, the model I discussed with you I used to assess diagn x age 
>> interactions, regressing out the effects of state and gender. However, 
>> in this model all interaction terms are incorporated. Is there a way 
>> to build the model only incorporating main effects of diagn, state, 
>> gender, age and diagn*age and diagn*state interactions? Since I do not 
>> expect any higher order interactions or state* age interactions, for 
>> instance (this is biologically not very plausible, although I did not 
>> formally test it).
>> 
>> Second, for areas where there is no diagn*age interaction I want to 
>> use a model without any interaction term with age, so I was thinking 
>> to use DOSS (I still want to regress out the effects of age, so it was 
>> added as a regressor):
>> 
>> diagn1*state1*gender1
>> 
>> diagn1*state1*gender2
>> 
>> diagn1*state2*gender1
>> 
>> diagn1*state2*gender2
>> 
>> diagn2*state1*gender1
>> 
>> diagn2*state1*gender2
>> 
>> diagn2*state2*gender1
>> 
>> diagn2*state2*gender2
>> 
>> age
>> 
>> However, here there are still interaction terms with gender in the 
>> model. I do want to regress out the effects of gender (since I expect 
>> this to be a confounder), without incorporating the interaction term. 
>> How should I do this? The only solution I can think of is building a 
>> model with gender as additional regressor (containing 0 en 1) and 
>> using DOSS. So:
>> 
>> diagn1*state1
>> 
>> diagn1*state2
>> 
>> diagn2*state1
>> 
>> diagn2*state2
>> 
>> age
>> 
>> gender
>> 
>> Does this make sense?
>> 
>> Third, if so, it implies that for areas where there is no diagn*state 
>> interaction, and where I want to test diagn1 vs diagn2 (regressing out 
>> the effects of state, since I expect this to be a confounder), I 
>> should again build a new model:
>> 
>> diagn1
>> 
>> diagn2
>> 
>> age
>> 
>> gender
>> 
>> state
>> 
>> I realize this is a lot of work, hence I hope you could give me 
>> any advice about this.
>> 
>> Thanks,
>> 
>> Maaike
>> 
>> 
>> From: r_maa...@hotmail.com
>> To: freesurfer@nmr.mgh.harvard.edu
>> Date: Tue, 3 Feb 2015 13:18:55 +0100
>> Subject: Re: [Freesurfer] average values per cluster
>> 
>> Hi Doug,
>> 
>> Sorry, the statistician doesn't understand it yet; we're currently 
>> building freesurfer and SPSS models step by step to find out what's 
>> going on, but it's a litte time consuming... so, to be continued!
>> 
>> Maaike
>> 
>> 
>> From: r_maa...@hotmail.com
>> To: freesurfer@nmr.mgh.harvard.edu
>> Date: Fri, 30 Jan 2015 20:55:27 +0100
>> Subject: Re: [Freesurfer] average values per cluster
>> 
>> On second thought, I think the reason for the discrepancy is that I 
>> included state as a factor instead of covariate in the SPSS model. I 
>> ran the model again after having adjusted this and included every 
>> possible interaction; now I reach a p value of 0.009 (which is still 
>> different but at least significant). But I'll check again Monday!
>> 
>> 
>> From: r_maa...@hotmail.com
>> To: freesurfer@nmr.mgh.harvard.edu
>> Date: Fri, 30 Jan 2015 20:15:07 +0100
>> Subject: Re: [Freesurfer] average values per cluster
>> 
>> I thought so, but I will check with the statistician next Monday, I'll 
>> get back to you as soon as I'm sure.
>> 
>> 
>> Date: Fri, 30 Jan 2015 14:12:32 -0500
>> From: gr...@nmr.mgh.harvard.edu
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] average values per cluster
>> 
>> 
>> Actually, that looks correct. Is this what you fed to SPSS?
>> 
>> On 1/30/15 2:07 PM, maaike rive wrote:
>> 
>>Ok, I'm so sorry, I'm afraid I mixed things up. I indeed used
>>DODS, and assumed these were may regressors:
>> 
>>diagn1*state1*gender1
>> 
>>diagn1*state1*gender2
>> 
>>diagn1*state2*gender1
>> 
>>diagn1*state2*gender2
>> 
>>diagn2*state1*gender1
>> 
>>diagn2*state1*gender2
>> 
>>diagn2*state2*gender1
>> 
>>diagn2*state2*gender2
>> 
>>diagn1*state1*gender1*age
>> 
>>diagn1*state1*gender2*age
>> 
>>diagn1*state2*gender1*age
>> 
>>diagn1*state2*gender2*age
>> 
>>diagn2*state1*gender1*age
>> 
>>diagn2*state1*gender2*age
>> 
>>diagn2*state

Re: [Freesurfer] longitudinal tracula error

[Anastasia Yendiki]

Hi Francesco - Please attach your dmrirc, and also the tracula log file of 
your subject (scripts/trac-all.log). It's hard to guess what went wrong 
without looking at the complete output.


Thanks,
a.y

On Thu, 29 Jan 2015, Francesco Siciliano wrote:


Hi,
I have been unsuccessful in getting longitudinal tracula to run. I have been 
directing my dmrirc file to skip the registration-based B0-inhomogeneity 
compensation (by setting it to 0).
However, when I try to run trac-all prep, I get an error message asking to 
specify a field map for each input. I also tried running the step and 
specifying appropriate field maps, yet
still got the same error. Any help with this would be appreciated.

Best,


Francesco Siciliano, B.A. Research Assistant
Department of Child and Adolescent Psychiatry
The New York State Psychiatric Institute
Columbia University
1051 Riverside Drive, Unit 74
New York, NY 10032
(646) 774-5703

___
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] bbregister error [Was: TRACULA mask error]

[Douglas N Greve]

or --init-rr if you don't have matlab/spm

On 02/06/2015 01:49 PM, Bruce Fischl wrote:
> try --init-spm
> On Fri, 6 Feb 2015, Anastasia Yendiki wrote:
>
>>
>> Hi Amanda - So it looks like --init-header didn't work, and neither does
>> --init-fsl. I'll defer to the father of bbregister, Doug, for clues 
>> about
>> how to proceed.
>>
>> a.y
>>
>> On Wed, 21 Jan 2015, Worker, Amanda wrote:
>>
>>> Hi Anastasia,
>>>
>>> Yes I have done that. My command line was... " bbregister --s 
>>> PDPLUS010 --init-header --dti --mov 
>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz
>>>  
>>> --reg 
>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat
>>>  
>>> --fslmat 
>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat
>>>  
>>> "
>>>
>>> Following the instructions printed I can only see a tiny bit of the 
>>> dwi.nii.gz, as attached.
>>>
>>> I've also tried substituting --dti for --t1 in the command line and 
>>> that doesn't make much difference.
>>>
>>> Do you have any other ideas?
>>>
>>> Thanks,
>>>
>>> Amanda
>>>
>>>
>>>
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Anastasia 
>>> Yendiki 
>>> Sent: 15 January 2015 15:36
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>
>>> Did you follow the instructions and the end of the output of the
>>> bbregister command? What does that look like? See what I wrote below 
>>> about
>>> looking for the bbregister command in trac-all.log, running it 
>>> separately
>>> on one subject after changing that one option and looking at its 
>>> output.
>>>
>>> On Wed, 14 Jan 2015, Worker, Amanda wrote:
>>>
 Sorry, I misunderstood.

 I've attached a screenshot of what I can see, it does look like 
 there is probably a different problem now as both the 
 dtifit_FA.nii.gz and aparc+aseg.bbr.nii are completely off centre.

 Thanks,

 Amanda


 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
  on behalf of Anastasia 
 Yendiki 
 Sent: 13 January 2015 17:52
 To: Freesurfer support list
 Subject: Re: [Freesurfer] TRACULA mask error

 It's impossible to know unless you actually check the registration. 
 See my
 previous email below on how to do that.

 On Tue, 13 Jan 2015, Worker, Amanda wrote:

> I have edited the trac-preproc script to "--init-header" instead 
> of "--init-fsl" - hoping that this would fix the registration 
> problem. Perhaps this hasn't helped?
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia 
> Yendiki 
> Sent: 12 January 2015 19:58
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA mask error
>
> Have you checked that the registration has been fixed? It looks 
> like it
> might not.
>
> On Mon, 12 Jan 2015, Worker, Amanda wrote:
>
>> Yes of course. Please find attached.
>>
>> Thanks,
>>
>> Amanda
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Anastasia 
>> Yendiki 
>> Sent: 12 January 2015 16:39
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA mask error
>>
>> Can you please attach the entire trac-all.log file? It's hard to 
>> tell just
>> from the last few lines, the initial error may have happened much 
>> earlier.
>>
>> On Mon, 12 Jan 2015, Worker, Amanda wrote:
>>
>>> Hi Anastasia,
>>>
>>> Thank you for your response. I have made the changes that you 
>>> recommended and attempted to run trac-all -prep on one of the 
>>> subjects with errors. I am now getting the following error:
>>>
>>> Writing output files to 
>>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_*
>>> Writing spline volumes to 
>>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz
>>> Segmentation fault
>>>
>>> trac-preproc-edit exited with ERRORS at Fri Jan
>>>
>>>
>>> Do you have any idea what the problem could be now?
>>>
>>> Thanks,
>>>
>>> Amanda
>>>
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia 
>>> Yendiki [ayend...@nmr.mgh.harvard.edu]
>>> Sent: 07 January 2015 17:11
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>
>>> Hi Amanda - See attached screenshot of your data, there is a gross
>>> misregistration (~45 degree angle rotation) between the 
>>> diffusion and
>>> anatomical. You can chec

Re: [Freesurfer] bbregister error [Was: TRACULA mask error]

[Anastasia Yendiki]

Hi Amanda - So it looks like --init-header didn't work, and neither does 
--init-fsl. I'll defer to the father of bbregister, Doug, for clues about 
how to proceed.

a.y

On Wed, 21 Jan 2015, Worker, Amanda wrote:

> Hi Anastasia,
>
> Yes I have done that. My command line was... " bbregister --s PDPLUS010 
> --init-header --dti --mov 
> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz 
> --reg 
> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat
>  --fslmat 
> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat
>  "
>
> Following the instructions printed I can only see a tiny bit of the 
> dwi.nii.gz, as attached.
>
> I've also tried substituting --dti for --t1 in the command line and that 
> doesn't make much difference.
>
> Do you have any other ideas?
>
> Thanks,
>
> Amanda
>
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: 15 January 2015 15:36
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA mask error
>
> Did you follow the instructions and the end of the output of the
> bbregister command? What does that look like? See what I wrote below about
> looking for the bbregister command in trac-all.log, running it separately
> on one subject after changing that one option and looking at its output.
>
> On Wed, 14 Jan 2015, Worker, Amanda wrote:
>
>> Sorry, I misunderstood.
>>
>> I've attached a screenshot of what I can see, it does look like there is 
>> probably a different problem now as both the dtifit_FA.nii.gz and 
>> aparc+aseg.bbr.nii are completely off centre.
>>
>> Thanks,
>>
>> Amanda
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Anastasia Yendiki 
>> 
>> Sent: 13 January 2015 17:52
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA mask error
>>
>> It's impossible to know unless you actually check the registration. See my
>> previous email below on how to do that.
>>
>> On Tue, 13 Jan 2015, Worker, Amanda wrote:
>>
>>> I have edited the trac-preproc script to "--init-header" instead of 
>>> "--init-fsl" - hoping that this would fix the registration problem. Perhaps 
>>> this hasn't helped?
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Anastasia Yendiki 
>>> 
>>> Sent: 12 January 2015 19:58
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>
>>> Have you checked that the registration has been fixed? It looks like it
>>> might not.
>>>
>>> On Mon, 12 Jan 2015, Worker, Amanda wrote:
>>>
 Yes of course. Please find attached.

 Thanks,

 Amanda
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
  on behalf of Anastasia Yendiki 
 
 Sent: 12 January 2015 16:39
 To: Freesurfer support list
 Subject: Re: [Freesurfer] TRACULA mask error

 Can you please attach the entire trac-all.log file? It's hard to tell just
 from the last few lines, the initial error may have happened much earlier.

 On Mon, 12 Jan 2015, Worker, Amanda wrote:

> Hi Anastasia,
>
> Thank you for your response. I have made the changes that you recommended 
> and attempted to run trac-all -prep on one of the subjects with errors. I 
> am now getting the following error:
>
> Writing output files to 
> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_*
> Writing spline volumes to 
> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz
> Segmentation fault
>
> trac-preproc-edit exited with ERRORS at Fri Jan
>
>
> Do you have any idea what the problem could be now?
>
> Thanks,
>
> Amanda
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: 07 January 2015 17:11
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA mask error
>
> Hi Amanda - See attached screenshot of your data, there is a gross
> misregistration (~45 degree angle rotation) between the diffusion and
> anatomical. You can check if this is the case for the rest of your bad
> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical
> segmentation mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii).
>
> According to bbregister czar Doug, a big error like this in bbregister
> happens when the initialization of the registration fails. If the
> diffusion and T1 were acquired in the same session, you can try
> initializing the registration from the headers of the images, by runni

Re: [Freesurfer] TRACULA bvec question

[Anastasia Yendiki]

Hi Jennifer - It lookes like bedpostx failed. Can you try running bedpostx 
directly like this and sending the output?

bedpostx {subject's directory}/dmri

Thanks,
a.y

On Thu, 22 Jan 2015, Jennifer Farren wrote:


Hey Anastasia! We have been chugging along since we last spoke but have 
encountered a brand new problem. For
about half of our subjects, Tracula seems to be running just fine and it spits 
out the appropriate output, but
for the other half we seem to be having a problem with it filling the directory 
with about 49 gzipped nifti's of
both data_slice_00**.nii.gz and nodif_brain_mask_slice_00**.nii.gz images in 
the subject's dmri folder. 
We are calling the bedpostx function directly. When it runs, it only takes about 25 
seconds and it says:"Making
bedpostx directory structure
 Queuing preprocessing stages
 Queuing parallel processing stage
 0 slices processed
 Queuing post processing stage"

After it's "completed" the dmri folder is filled with those gzipped nifti 
slices.

And I'm not sure if this may narrow down the problem but I became aware of the 
bad output by an error during the
-path stage of Tracula which says: 
"niiRead(): error opening file {subject's 
directory}/dmri.bedpostX/merged_ph1samples.nii.gz 
 ERROR: Could not read {subject's 
directory}/dmri.bedpostX/merged_ph1samples.nii.gz"

This error makes sense since the bedpostx function is not completing correctly. 
However, it's peculiar that this
error only affects about half of the subjects. Have you encountered this 
problem before? Do you have a hunch as
to what might cause it? I'm attaching a screenshot of a subject's dmri folder 
that ran properly and a screenshot
of the same directory of a subject that did not run properly.

Thanks for your help!!

-freesurfer-boun...@nmr.mgh.harvard.edu wrote: -To: Freesurfer support 
list

From: Anastasia Yendiki
Sent by: freesurfer-boun...@nmr.mgh.harvard.edu
Date: 01/05/2015 08:20PM
Subject: Re: [Freesurfer] TRACULA bvec question

Hi Jennifer - You're very welcome, thank you for trying out TRACULA!

About the eigenvectors: what software are you using to visualize the
lines? Unfortunately freeview in version 5.3 has a bug in the vector
display, so it may show the vectors wrong when they are not.

About those few cases where a tract looks like a single curve: It can
happen sometimes when the anatomy is a bit tricky, and you may be able to
fix it by reinitializing the tractography. To do this, you set reinit = 1
in your configuration file, set your subjlist and pathlist only to the
specific subject/tract combination that fails, and rerun the -prior and
-path steps. This is described also at the very bottom of the example
configuration file, $FREESURFER_HOME/bin/dmrirc.example.

Hope this helps,
a.y


  On Mon, 5 Jan 2015, Jennifer Farren wrote:

> Hello TRACULA experts,
>
> Thank you very much for this wonderful resource. Our team is using TRACULA
> for the first time to analyze our DTI data.
>
> We're running into a few issues and our questions are as follows:
>
> 1) After running TRACULA on our subjects, we were doing some final quality
> control checks and noticed that the primary eigenvectors are not aligned in
> the direction you would expect (see the image "Subject 005 Misaligned
> Eigenvectors" attached of one subject's dtifit_FA.nii.gz and
> dtifti_V1.nii.gz in freeview). Nevertheless, our data looks pretty good
> altogether.  None of the tracts look flipped or blatantly wrong (aside from
> the problem below). We noticed from the listserv, that you said the tracts
> will look visibly wrong if the bvecs aren't oriented properly (Listserv
> Thread). Could you shed any light on what is going on here? We are rerunning
> the subjects with transposed bvecs now which should fix the problem.
>
> 2) Also, in our final output we do end up getting some hairline tracts,
> where when uploading the bbr tract file in freeview, it looks like a single
> fiber (see the images "Subject 031 FMajor - View 1" and "Subject 031 FMajor
> - View 2" attached). What might be causing this? It doesn't appear very
> often. Is it a significant problem in our processing, or can we just throw
> away the stats for that specific subject's tract? Will this be fixed by
> accounting for motion or rerunning with the transposed bvecs?
>
> Thank you for your time!
>
> Best,
>
> The Solomon Lab Team
>
>
___
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] applyMorph to 3d voxel coordinate list

[Zachary Greenberg]

Freesurfers,

I'm trying to apply a non-linear warping calculated using mri_cvs_register
to a list of 3d voxel coordinates. There doesn't appear to be much
documentation on this function, but someone else on the forum suggested I
add an input 'point_list' with the coordinates.

Does anyone know what format point_list should be? Trying this with a .txt
file with the coordinates xyz as space separated columns returns a text
file with every row containing the same coordinate, so I'm assuming my
formatting is incorrect.

Thanks for any help you can offer,

-zack

-- 
*Zachary Greenberg*
*Imaging Specialist*
*Department of Neurological Surgery*
*University of California, San Francisco*
___
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] bbregister error [Was: TRACULA mask error]

[Bruce Fischl]

try --init-spm
On Fri, 6 Feb 2015, Anastasia Yendiki wrote:

>
> Hi Amanda - So it looks like --init-header didn't work, and neither does
> --init-fsl. I'll defer to the father of bbregister, Doug, for clues about
> how to proceed.
>
> a.y
>
> On Wed, 21 Jan 2015, Worker, Amanda wrote:
>
>> Hi Anastasia,
>>
>> Yes I have done that. My command line was... " bbregister --s PDPLUS010 
>> --init-header --dti --mov 
>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz
>>  --reg 
>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat
>>  --fslmat 
>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat
>>  "
>>
>> Following the instructions printed I can only see a tiny bit of the 
>> dwi.nii.gz, as attached.
>>
>> I've also tried substituting --dti for --t1 in the command line and that 
>> doesn't make much difference.
>>
>> Do you have any other ideas?
>>
>> Thanks,
>>
>> Amanda
>>
>>
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Anastasia Yendiki 
>> 
>> Sent: 15 January 2015 15:36
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA mask error
>>
>> Did you follow the instructions and the end of the output of the
>> bbregister command? What does that look like? See what I wrote below about
>> looking for the bbregister command in trac-all.log, running it separately
>> on one subject after changing that one option and looking at its output.
>>
>> On Wed, 14 Jan 2015, Worker, Amanda wrote:
>>
>>> Sorry, I misunderstood.
>>>
>>> I've attached a screenshot of what I can see, it does look like there is 
>>> probably a different problem now as both the dtifit_FA.nii.gz and 
>>> aparc+aseg.bbr.nii are completely off centre.
>>>
>>> Thanks,
>>>
>>> Amanda
>>>
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Anastasia Yendiki 
>>> 
>>> Sent: 13 January 2015 17:52
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>
>>> It's impossible to know unless you actually check the registration. See my
>>> previous email below on how to do that.
>>>
>>> On Tue, 13 Jan 2015, Worker, Amanda wrote:
>>>
 I have edited the trac-preproc script to "--init-header" instead of 
 "--init-fsl" - hoping that this would fix the registration problem. 
 Perhaps this hasn't helped?
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
  on behalf of Anastasia Yendiki 
 
 Sent: 12 January 2015 19:58
 To: Freesurfer support list
 Subject: Re: [Freesurfer] TRACULA mask error

 Have you checked that the registration has been fixed? It looks like it
 might not.

 On Mon, 12 Jan 2015, Worker, Amanda wrote:

> Yes of course. Please find attached.
>
> Thanks,
>
> Amanda
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: 12 January 2015 16:39
> To: Freesurfer support list
> Subject: Re: [Freesurfer] TRACULA mask error
>
> Can you please attach the entire trac-all.log file? It's hard to tell just
> from the last few lines, the initial error may have happened much earlier.
>
> On Mon, 12 Jan 2015, Worker, Amanda wrote:
>
>> Hi Anastasia,
>>
>> Thank you for your response. I have made the changes that you 
>> recommended and attempted to run trac-all -prep on one of the subjects 
>> with errors. I am now getting the following error:
>>
>> Writing output files to 
>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_*
>> Writing spline volumes to 
>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz
>> Segmentation fault
>>
>> trac-preproc-edit exited with ERRORS at Fri Jan
>>
>>
>> Do you have any idea what the problem could be now?
>>
>> Thanks,
>>
>> Amanda
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: 07 January 2015 17:11
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] TRACULA mask error
>>
>> Hi Amanda - See attached screenshot of your data, there is a gross
>> misregistration (~45 degree angle rotation) between the diffusion and
>> anatomical. You can check if this is the case for the rest of your bad
>> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical
>> segmentation mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii).
>>
>> According to bbregister czar Doug, a big error like this in bbregister
>> happ

Re: [Freesurfer] bvallist option in dmrirc file?

[Anastasia Yendiki]

Hi Janosch - I'd implement the option to exclude volumes for longitudinal 
data, but if you remove a different number from each time point I'd make 
sure it's randomized between time points. You don't want, for example, to 
always be removing more volumes from later than earlier time points (if 
your subjects' motion gets worse over time) because then you're 
introducing a bias.


About lme, you can use it for FA/MD/etc of different tracts or points 
along the tract, the way you would, let's say, for volumes of different 
subcortical stuctures. So each tract or point along the tract would be 
analyzed separately. There isn't anything custom implemented for along the 
tract stats in lme.


Hope this helps,
a.y

On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote:


Hi Anastasia,

Am 15.01.2015 um 16:14 schrieb Anastasia Yendiki :



Sorry, I misunderstood. You have different numbers of directions not only 
between subjects, but also between time points of the same subject?


Yes, sadly. There a children who did good on some measurement time points and 
not so good on others...


I wouldn't recommend that. If your scans differ between time points, it'll be 
impossible to tell whether within-subject changes that you find are due to 
changes in the acquisition or actual changes in the brain.



Yes, it's at least questionable. So, would you also not implement the future 
option to exclude volumes for longitudinal tracula?

BTW:

- can I use the lme toolbox to do longitudinal statistics on the tracts 
identified by tracula or do I need the same number of dti scans for every 
subject?
- If so, does it also work for statistics along the trajectory of a tract?

Thanks a lot,

Janosch


On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote:


Hi Anastasia,

I am already preparing separate dmrirc files for different subjects (but 
including all time points for a specific subject) because that way I can run 
them in parallel on different cores.

I thought it was important to have all time points of a subject in one dmrirc file. If I 
understand you correctly, it's OK to have them in separate ones? Is the only thing that's 
needed to indicate longitudinal processing the "baselist" variable?

If so, it would be great because I could run even more processes in parallel :)

Thanks,

Janosch

Am 15.01.2015 um 15:51 schrieb Anastasia Yendiki :



Hi Janosch - This makes sense. I do want to incorporate support for the case 
where volumes are discarded for quality reasons in the next version, but it's 
not possible in the current version unfortunately. You'll have to generate 
separate config files for each case. Sorry for the hassle!

a.y

On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote:


Hi Anastasia,

in principle, all subjects were scanned with the same b-values (and bvecs for 
that matter). But as it is a pediatric sample, some of them don't have all 
volumes (67), because scans had to be aborted. We used a sequence that 
distributes the directions in a way that the data from aborted scans should 
still be processable.

So, what I was trying to do was shorten the bvals (and bvecs) files to the 
length of the respective run (e.g., if it only has 54 volumes, the bvals and 
bvecs files are shortened to 54 lines) and include them on a per subject 
basis...

Thanks,

Janosch


Hi Janosch - Yes, it assumes that all subjects in your study where scanned with 
the same b-values. What is your situation?
a.y

On Thu, 15 Jan 2015, Janosch Linkersdörfer wrote:


Hi,

I am trying to process diffusion data with the longitudinal TRACULA stream. I
want to specify different bvecs and bvals files per scan in the dmrirc file.

For bvecs this is possible using

bveclist = ...

I tried to use

bvallist = ...

but apparently this does not seem to work because trac-all complains that no
b-value file has been specified.

Can only one bvalfile be specified for all scans?

Thanks,

Janosch







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








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


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

Re: [Freesurfer] topology defect in freesurfer

[Lilla Zollei]

Hi Shaheen,

Freesurfer does not handle that age-range so it is not applicable for 
neonates.


Send me an email and I will tell you what we are developing now that might 
be appropriate for you.


Lilla

On Fri, 6 Feb 2015, Shaheen Ahmed wrote:


Hello,

 I am using freesurfer for neonates but get error at the topology construction 
(excessive topological defect encountered, could not allocate edges for 
retesselation). My question is 
1) is the freesurfer applicable for neonates? I have tried it for 2 year to 9 
year old kid it worked fine.
2) I tried the -old fixer flag and tried to run the recon -all but i get the 
same error.

Any suggestions are appreciated.

Thanks,
Shaheen

_

UT Southwestern

Medical Center

The future of medicine, today.


___
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] topology defect in freesurfer

[Shaheen Ahmed]

Hello,

 I am using freesurfer for neonates but get error at the topology construction 
(excessive topological defect encountered, could not allocate edges for 
retesselation). My question is
1) is the freesurfer applicable for neonates? I have tried it for 2 year to 9 
year old kid it worked fine.
2) I tried the -old fixer flag and tried to run the recon -all but i get the 
same error.

Any suggestions are appreciated.

Thanks,
Shaheen



UT Southwestern


Medical Center



The future of medicine, today.

___
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] Freeview colorbar with command line & white background?

[Ruopeng Wang]

Hi Xiuming,

You can’t change color scale or change the background color from the 
command-line. You can change the background color from the GUI: Edit -> 
Preferences. I will add these options in the command-line.

Best,
Ruopeng

On Feb 6, 2015, at 11:52 AM, Xiuming Zhang  wrote:

> Dear freesurfer experts,
> 
> I have two quick questions regarding freeview.
> 
> (1) The color bar is still from 0 to 1 even if I am overlying a super 
> small-valued (1e-6) map on lh.inflated. Here is what I did:
> 
> freeview -f lh.inflated:overlay=lh.map:overlay_method=linear:edgethickness=0 
> -viewport 3d -colorscale
> 
> In GUI, I can right click the colorbar and choose "Show colorer -> 
> lh.inflated". Is it possible to do it in command line?
> 
> (2) Is it possible to set the background to be white instead of black? It 
> would be great if it can also be automated (i.e., with command line). Here is 
> what I have so far.
> 
> freeview -f rh.inflated:overlay=rh.map -ss ./rh
> 
> Thank you very much in advance for your help!
> 
> Best regards,
> Xiuming
> 
> ᐧ
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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


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

[Freesurfer] Freeview colorbar with command line & white background?

[Xiuming Zhang]

Dear freesurfer experts,

I have two quick questions regarding freeview.

(1) The color bar is still from 0 to 1 even if I am overlying a super
small-valued (1e-6) map on lh.inflated. Here is what I did:

freeview -f
lh.inflated:overlay=lh.map:overlay_method=linear:edgethickness=0 -viewport
3d -colorscale

In GUI, I can right click the colorbar and choose "Show colorer ->
lh.inflated". Is it possible to do it in command line?

(2) Is it possible to set the background to be white instead of black? It
would be great if it can also be automated (i.e., with command line). Here
is what I have so far.

freeview -f rh.inflated:overlay=rh.map -ss ./rh

Thank you very much in advance for your help!

Best regards,
Xiuming

ᐧ
___
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] average values per cluster

[Douglas N Greve]

There is not a way to build more flexible models in the FSGD structure. 
However, you can create your own design matrix and include anything you 
want in it and pass it to mri_glmfit with --X instead of --fsgd.

doug

On 02/05/2015 06:13 AM, maaike rive wrote:
>
> Hi Doug,
>
> I hope I'm not driving you crazy, but I have some additional questions 
> regardig the DOSS/DODS models. Also because of the SPSS discrepancies.
>
> First, the model I discussed with you I used to assess diagn x age 
> interactions, regressing out the effects of state and gender. However, 
> in this model all interaction terms are incorporated. Is there a way 
> to build the model only incorporating main effects of diagn, state, 
> gender, age and diagn*age and diagn*state interactions? Since I do not 
> expect any higher order interactions or state* age interactions, for 
> instance (this is biologically not very plausible, although I did not 
> formally test it).
>
> Second, for areas where there is no diagn*age interaction I want to 
> use a model without any interaction term with age, so I was thinking 
> to use DOSS (I still want to regress out the effects of age, so it was 
> added as a regressor):
>
> diagn1*state1*gender1
>
> diagn1*state1*gender2
>
> diagn1*state2*gender1
>
> diagn1*state2*gender2
>
> diagn2*state1*gender1
>
> diagn2*state1*gender2
>
> diagn2*state2*gender1
>
> diagn2*state2*gender2
>
> age
>
> However, here there are still interaction terms with gender in the 
> model. I do want to regress out the effects of gender (since I expect 
> this to be a confounder), without incorporating the interaction term. 
> How should I do this? The only solution I can think of is building a 
> model with gender as additional regressor (containing 0 en 1) and 
> using DOSS. So:
>
> diagn1*state1
>
> diagn1*state2
>
> diagn2*state1
>
> diagn2*state2
>
> age
>
> gender
>
> Does this make sense?
>
> Third, if so, it implies that for areas where there is no diagn*state 
> interaction, and where I want to test diagn1 vs diagn2 (regressing out 
> the effects of state, since I expect this to be a confounder), I 
> should again build a new model:
>
> diagn1
>
> diagn2
>
> age
>
> gender
>
> state
>
> I realize this is a lot of work, hence I hope you could give me 
> any advice about this.
>
> Thanks,
>
> Maaike
>
> 
> From: r_maa...@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Tue, 3 Feb 2015 13:18:55 +0100
> Subject: Re: [Freesurfer] average values per cluster
>
> Hi Doug,
>
> Sorry, the statistician doesn't understand it yet; we're currently 
> building freesurfer and SPSS models step by step to find out what's 
> going on, but it's a litte time consuming... so, to be continued!
>
> Maaike
>
> 
> From: r_maa...@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Fri, 30 Jan 2015 20:55:27 +0100
> Subject: Re: [Freesurfer] average values per cluster
>
> On second thought, I think the reason for the discrepancy is that I 
> included state as a factor instead of covariate in the SPSS model. I 
> ran the model again after having adjusted this and included every 
> possible interaction; now I reach a p value of 0.009 (which is still 
> different but at least significant). But I'll check again Monday!
>
> 
> From: r_maa...@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Fri, 30 Jan 2015 20:15:07 +0100
> Subject: Re: [Freesurfer] average values per cluster
>
> I thought so, but I will check with the statistician next Monday, I'll 
> get back to you as soon as I'm sure.
>
> 
> Date: Fri, 30 Jan 2015 14:12:32 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] average values per cluster
>
>
> Actually, that looks correct. Is this what you fed to SPSS?
>
> On 1/30/15 2:07 PM, maaike rive wrote:
>
> Ok, I'm so sorry, I'm afraid I mixed things up. I indeed used
> DODS, and assumed these were may regressors:
>
> diagn1*state1*gender1
>
> diagn1*state1*gender2
>
> diagn1*state2*gender1
>
> diagn1*state2*gender2
>
> diagn2*state1*gender1
>
> diagn2*state1*gender2
>
> diagn2*state2*gender1
>
> diagn2*state2*gender2
>
> diagn1*state1*gender1*age
>
> diagn1*state1*gender2*age
>
> diagn1*state2*gender1*age
>
> diagn1*state2*gender2*age
>
> diagn2*state1*gender1*age
>
> diagn2*state1*gender2*age
>
> diagn2*state2*gender1*age
>
> diagn2*state2*gender2*age
>
>
> However what I actually meant to do was testing for the effects of
> diagnosis and interactions (e.g. diagnosis*age) by using the
> appropriate contrasts, so I thought that if I used the contrast
> for the diagnosis*age interaction, I was testing wh

Re: [Freesurfer] Freesurfer could not accurately recognize the voxel size

[Douglas N Greve]

It sounds like the voxel size is wrong. Where did you get the input 
volume from? If you load the input volume into tkmedit or freeview, how 
does it look? If you run mri_info on the input, what voxel size does it 
give?

On 02/06/2015 11:21 AM, Liu Y wrote:
> Hi Bruce,
> The full recon-all command line is "recon-all -cw256 -s T8_1 -all" and 
> the input format is mgz. The mgz file is created by running 
> recon-all -i. The 001.mgz under /mri/orig looks just normal, but when 
> complete the  "recon-all -cw256 -s T8_1 -all",  the orig.mgz was 
> re-scaled (stretched) in left-right direction, and could not see the 
> left and right boundaries of the brain.
> Thanks,
> Yawu
>
> On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Yawu
>
> what was the full recon-all command line? What is your input
> format? If
> all else fails you can mri_convert your input volume nifti or mgz and
> override what is in the header (e.g. mri_convert -iks 1 ...)
>
> cheers
> Bruce
> On Fri, 6 Feb
> 2015, Liu Y wrote:
>
> > Dear Experts,
> > When I run recon-all -cw256 -s problemcase -all, the program
> seems not able
> > accurately to recognize the voxel size in this problematic case,
> in other
> > cases there is no problem. The program gave a warning like this:
> >
> >
> 
> WARNING===
> > ==
> > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which
> cannot fit
> > in 256^3 mm^3 volume.
> > The resulting volume will have 338 slices.
> > If you find problems, please let us know
> (freesurfer@nmr.mgh.harvard.edu
> ).
> >
> 
> ===
> > ==
> >
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from
> /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz...
> > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (0, -1, 0)
> > j_ras = (0, 0, 1)
> > k_ras = (1, 0, 0)
> > Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels.
> > Data is conformed to 1 mm size and 338 voxels for all directions
> > changing data type from float to uchar (noscale = 0)...
> > MRIchangeType: Building histogram
> > Reslicing using trilinear interpolation
> > writing to
> /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz...
> >
> > 
> > ERROR! FOV=338.000 > 256
> > Include the flag -cw256 with recon-all!
> > Inspect orig.mgz to ensure the head is fully visible.
> > 
> >
> > Then I checked the orig.mgz, the image was re-scaled (stretched) in
> > left-right direction, and could not see the left and right
> boundaries of the
> > brain. The program said that the Original Data has (1, 1, 2) mm
> size, but
> > actually the voxel size is 1*1*1 mm3.
> >
> > The freesurfer version 5.3, Ubuntu 12.04
> >
> > Thanks,
> >
> > Yawu
> >
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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

Re: [Freesurfer] Freesurfer could not accurately recognize the voxel size

[Bruce Fischl]

and what was the recon-all -i command line? Does the rawavg.mgz look 
correct? You can send us whatever file you gave to recon-all -i and we'll 
see why it is being converted incorrectly, or you can try the mri_convert 
command line I gave below (check out mri_convert --help) to override the 
voxel size info we read out of the header


On Fri, 6 Feb 2015, Liu Y wrote:


Hi Bruce,The full recon-all command line is "recon-all -cw256 -s T8_1 -all"
and the input format is mgz. The mgz file is created by
running recon-all -i. The 001.mgz under /mri/orig looks just normal, but
when complete the  "recon-all -cw256 -s T8_1 -all",  the orig.mgz was
re-scaled (stretched) in left-right direction, and could not see the left
and right boundaries of the brain. 
Thanks,
Yawu

On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl 
wrote:
  Hi Yawu

  what was the full recon-all command line? What is your input
  format? If
  all else fails you can mri_convert your input volume nifti or
  mgz and
  override what is in the header (e.g. mri_convert -iks 1 ...)

  cheers
  Bruce
  On Fri, 6 Feb
  2015, Liu Y wrote:

  > Dear Experts,
  > When I run recon-all -cw256 -s problemcase -all, the program
  seems not able
  > accurately to recognize the voxel size in this problematic
  case, in other
  > cases there is no problem. The program gave a warning like
  this:
  >
  
>WARNING====
  ===
  > ==
  > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm),
  which cannot fit
  > in 256^3 mm^3 volume.
  > The resulting volume will have 338 slices.
  > If you find problems, please let us know
  (freesurfer@nmr.mgh.harvard.edu).
  
>===

  > ==
  >
  > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp
  $
  > reading from
  /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz...
  > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00
  > i_ras = (0, -1, 0)
  > j_ras = (0, 0, 1)
  > k_ras = (1, 0, 0)
  > Original Data has (1, 1, 2) mm size and (240, 240, 169)
  voxels.
  > Data is conformed to 1 mm size and 338 voxels for all
  directions
  > changing data type from float to uchar (noscale = 0)...
  > MRIchangeType: Building histogram
  > Reslicing using trilinear interpolation
  > writing to
  /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz...
  >
  > 
  > ERROR! FOV=338.000 > 256
  > Include the flag -cw256 with recon-all!
  > Inspect orig.mgz to ensure the head is fully visible.
  > 
  >
  > Then I checked the orig.mgz, the image was re-scaled
  (stretched) in
  > left-right direction, and could not see the left and right
  boundaries of the
  > brain. The program said that the Original Data has (1, 1, 2)
  mm size, but
  > actually the voxel size is 1*1*1 mm3.
  >
  > The freesurfer version 5.3, Ubuntu 12.04
  >
  > Thanks,
  >
  > Yawu
  >
  >
  >
  >
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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



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


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

Re: [Freesurfer] I got error building with Read-only source.

[Z K]

Hello Jiho,

Freesurfer is a large complex software package with many 3rd party 
dependencies. Building it outside the Martinos Center can be a difficult 
task.

That being said, it is not impossible. I believe the issue you are 
encountering is related to a hard-coded path bug in the mni tools 
installation. To fix the error, I *beleive* you will need to create a 
directory on your machine called "/usr/pubsw/packages". Inside the 
"packages" directory you will need a create a symlink called "mni" which 
points to the location in which you installed mni, namely 
"/home/yjh0719/pubsw/packages/mni". In essence you need to do the following:

$> mkdir -p /usr/pubsw/packages
$> cd /usr/pubsw/packages
$> ln -s /home/yjh0719/pubsw/packages/mni ./mni

Please do the above and see if it helps take care of the issue.

-Zeke


On 02/05/2015 06:50 PM, Jiho Yeom wrote:
> Dear all.
>
> Hi. I am new to FreeSurfer.
>
> I am trying to build Read-only source.
>
> I followed the instructions in these pages:
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
>
> However I got these error messages.
>
> make[2]: Entering directory `/home/yjh0719/FreeSurferDev/dev/gpu_utils'
>
> /bin/sh ../libtool --tag=CXX --mode=link g++-L/usr/lib64
> -L/usr/X11R6/lib64
> -L/home/yjh0719/pubsw/packages/mni/1.4/lib
> -L/home/yjh0719/pubsw/packages/vxl/current/lib-o cudadetect
> -rdynamic -ldl cudadetect-cudadetect.o -L/usr/local/cuda/lib64 -lcuda
> -lcudart -lz -lm -lcrypt -ldl -lpthread
> /home/yjh0719/pubsw/packages/mni/1.4/lib/libnetcdf.a -lvolume_io -lminc
> -lvnl_algo -lvnl -lvcl  -lnetlib
> -lv3p_netlib
>
> libtool: link: warning: library
> `/home/yjh0719/pubsw/packages/mni/1.4/lib/libvolume_io.la
> ' was moved.
>
> libtool: link: warning: library
> `/home/yjh0719/pubsw/packages/mni/1.4/lib/libminc.la ' was
> moved.
>
> libtool: link: warning: library
> `/home/yjh0719/pubsw/packages/mni/1.4/lib/libvolume_io.la
> ' was moved.
>
> libtool: link: warning: library
> `/home/yjh0719/pubsw/packages/mni/1.4/lib/libminc.la ' was
> moved.
>
> libtool: link: cannot find the library
> `/usr/pubsw/packages/mni/1.4/lib/libnetcdf.la ' or
> unhandled argument `/usr/pubsw/packages/mni/1.4/lib/libnetcdf.la
> '
>
> make[2]: *** [cudadetect] Error 1
>
> make[2]: Leaving directory `/home/yjh0719/FreeSurferDev/dev/gpu_utils'
>
> make[1]: *** [all-recursive] Error 1
>
> make[1]: Leaving directory `/home/yjh0719/FreeSurferDev/dev'
>
> make: *** [all] Error 2
>
> It seems that libtool cannot find the library.
>
> I set the mni path to be /home/yjh0719/pubsw/packages/mni/1.4/lib/, so
> it has to be started with /home/yjh0719/pubsw/…, but it finds
> /usr/pubsw/packages/
>
> I tried to find path string starts with ‘/usr/pubsw/packages’ in
> Makefiles, and change it into ‘/home/yjh0719/…’, but it still cannot find.
>
> What am I supposed to do with this problem?
>
> I hope someone can help me.
>
> Thanks.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Freesurfer could not accurately recognize the voxel size

[Liu Y]

Hi Bruce,
The full recon-all command line is "recon-all -cw256 -s T8_1 -all" and the
input format is mgz. The mgz file is created by running recon-all -i.
The 001.mgz
under /mri/orig looks just normal, but when complete the  "recon-all -cw256
-s T8_1 -all",  the orig.mgz was re-scaled (stretched) in left-right
direction, and could not see the left and right boundaries of the brain.
Thanks,
Yawu

On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl 
wrote:

> Hi Yawu
>
> what was the full recon-all command line? What is your input format? If
> all else fails you can mri_convert your input volume nifti or mgz and
> override what is in the header (e.g. mri_convert -iks 1 ...)
>
> cheers
> Bruce
> On Fri, 6 Feb
> 2015, Liu Y wrote:
>
> > Dear Experts,
> > When I run recon-all -cw256 -s problemcase -all, the program seems not
> able
> > accurately to recognize the voxel size in this problematic case, in other
> > cases there is no problem. The program gave a warning like this:
> >
> >
> WARNING===
> > ==
> > The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which cannot
> fit
> > in 256^3 mm^3 volume.
> > The resulting volume will have 338 slices.
> > If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu
> ).
> >
> ===
> > ==
> >
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz...
> > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (0, -1, 0)
> > j_ras = (0, 0, 1)
> > k_ras = (1, 0, 0)
> > Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels.
> > Data is conformed to 1 mm size and 338 voxels for all directions
> > changing data type from float to uchar (noscale = 0)...
> > MRIchangeType: Building histogram
> > Reslicing using trilinear interpolation
> > writing to /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz...
> >
> > 
> > ERROR! FOV=338.000 > 256
> > Include the flag -cw256 with recon-all!
> > Inspect orig.mgz to ensure the head is fully visible.
> > 
> >
> > Then I checked the orig.mgz, the image was re-scaled (stretched) in
> > left-right direction, and could not see the left and right boundaries of
> the
> > brain. The program said that the Original Data has (1, 1, 2) mm size, but
> > actually the voxel size is 1*1*1 mm3.
> >
> > The freesurfer version 5.3, Ubuntu 12.04
> >
> > Thanks,
> >
> > Yawu
> >
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2

[Douglas N Greve]

Look here
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
and get the appropriate mri_segstats for your system. Copy it to 
$FREESURFER_HOME/bin, rehash, and rerun

doug

On 02/06/2015 08:07 AM, Roberto Medeiros de Souza wrote:
> Hi,
> I'm knew to FreeSurfer. I am using the stable v5.3 and I am having the 
> known issue about
> "Creation of the aseg.stats table fails when only running -autorecon1 
> or -autorecon2 because ribbon.mgz is not present." The FreeSurfer page 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) says that 
> this problem has been solved and that I should ask for a patch. Does 
> anyone knows where I can get this patch?
>
>
> Thanks in advance!
>
> Roberto Medeiros de Souza
>
>
>
> ___
> 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] V1 masking

[Douglas N Greve]

Try using the --label-stat statvol option


On 02/06/2015 04:12 AM, David Soto wrote:
> Hi,
> I have been succesfully using mri_label2vol on the V1.labels to get a 
> nii file
> (i.e. mri_label2vol --label rh.V1.label  --temp 
> $SUBJECTS_DIR/$i/mri/orig/001 --identity --o rV1.nii --subject $i 
> --hemi rh --proj frac 0 1 0.01)
>
>
> but now I would like to use the "v1.prob.label" to get a .nii file 
> that  includes the probabilities of a voxel being on V1.
>
> is this possible?
>
> many thanks!
> david
>
>
>
> ___
> 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] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas N Greve]

It should be 10^-abs(sig)


On 02/06/2015 12:53 AM, Bronwyn Overs wrote:
> Hi Doug,
>
> Thanks for all of your help. I am investigating the differences 
> between the design matrices now.
>
> I have one more query about the sig.table.dat file put out by the GLM 
> using the parcellated ROIs. When I transform each of the values in 
> this file to p values using 10^"value", some of the resulting p-value 
> are >1. Do you know why this would be happening? Here is an example of 
> one of my sig.table.dat files, where 10^.799 = 6.295:
>
> lh.aparc.thicknessme_gender_ageRem me_group_ageRem
> lh_bankssts_thickness   0.107  -2.752
> lh_caudalanteriorcingulate_thickness  -2.616  -0.190
> lh_caudalmiddlefrontal_thickness   -0.701  -4.258
> lh_cuneus_thickness 0.799  -1.178
> lh_entorhinal_thickness 1.669  -4.129
> lh_fusiform_thickness  -0.088  -6.808
> lh_inferiorparietal_thickness  -0.665  -1.477
> lh_inferiortemporal_thickness   0.149  -7.985
> lh_isthmuscingulate_thickness  -0.476  -2.393
> lh_lateraloccipital_thickness   0.212  -1.189
> lh_lateralorbitofrontal_thickness   0.288  -7.657
> lh_lingual_thickness1.148  -1.594
> lh_medialorbitofrontal_thickness1.405  -4.461
> lh_middletemporal_thickness 0.727  -7.215
> lh_parahippocampal_thickness   -1.059  -2.854
> lh_paracentral_thickness   -0.514  -0.282
> lh_parsopercularis_thickness0.444  -3.541
> lh_parsorbitalis_thickness -0.110  -7.075
> lh_parstriangularis_thickness   0.244  -4.769
> lh_pericalcarine_thickness  0.376  -0.218
> lh_postcentral_thickness   -0.485  -0.832
> lh_posteriorcingulate_thickness-0.135  -1.241
> lh_precentral_thickness 0.196  -2.102
> lh_precuneus_thickness  0.018  -1.361
> lh_rostralanteriorcingulate_thickness  -1.208  -2.073
> lh_rostralmiddlefrontal_thickness   0.437  -4.470
> lh_superiorfrontal_thickness   -0.141  -2.743
> lh_superiorparietal_thickness  -0.288  -0.365
> lh_superiortemporal_thickness   0.227  -4.646
> lh_supramarginal_thickness -1.185  -1.354
> lh_frontalpole_thickness   -0.325  -0.521
> lh_temporalpole_thickness  -0.067  -4.074
> lh_transversetemporal_thickness-0.009  -1.618
> lh_insula_thickness 0.553  -6.063
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au 
>
> Follow @neuraustralia on twitter 
> Follow NeuRA on facebook 
> Subscribe to 
> the NeuRA Magazine 
>
> On 5/02/2015 10:46 am, Douglas N Greve wrote:
>> How sure are you that you are using the exact same model? Can you output
>> the design matrix from SPSS? Can you input the FS design matrix into
>> SPSS? Are you sure you are using the exact same input data?
>>
>> On 02/04/2015 06:32 PM, Bronwyn Overs wrote:
>>> Ahh right. I have just understood which part of the output I needed to
>>> look at. However, for the ROI GLM there are only 1-2 regions that were
>>> significantly different between groups, while the SPSS ANCOVA showed
>>> significant group differences for the majority of parcellated regions.
>>> I have confirmed that I am using the exact same model for each, so it
>>> is only the analysis method that differs. Do you know why these two
>>> methods would produce such disparate results?
>>>
>>>
>>> Kind regards,
>>>
>>> Bronwyn Overs
>>> Research Assistant
>>>
>>> Neuroscience Research Australia
>>>
>>> Neuroscience Research Australia
>>> Margarete Ainsworth Building
>>> Barker Street Randwick Sydney NSW 2031 Australia
>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>
>>> neura.edu.au
>>>
>>> Follow @neuraustralia on twitter
>>> Follow NeuRA on facebook
>>> Subscribe to
>>> the NeuRA Magazine
>>>
>>> On 5/02/2015 3:16 am, Douglas N Greve wrote:
 I'm not sure that I understand what I'm looking at. If it is an ROI
 analysis, then there is no surface, it should be about 40 numbers, one
 for each ROI.

 On 02/03/2015 06:26 PM, Bronwyn Overs wrote:
> Hi Doug,
>
> Thanks for your correction.
>
> I have now completed the FDR for my case-control comparisons, and it
> appears that none of the regions survived. This is again quite
> confusing given the large number of parcellated regions that survived
> FDR in the SPSS ANCOVA. Can you confirm that this screenshot of the
> sig.mgh file from ROI analysis

Re: [Freesurfer] tksurfer

[Z K]

Please refrain from sending your license file out publicly to the 
freesurfer mailing list.

Your license file looks corrupted. I will email you a new one momentarily.

-Zeke

On 02/06/2015 10:43 AM, André Schmidt wrote:
> Thank you.
>
> I've changed the file to license.txt (see attached) and tried "chmod -R
> a+x /Applications/freesurfer/license" from the terminal, but got the
> message "chmod: Unable to change file mode on
> /Applications/freesurfer/license: Operation not permitted".
>
> Do you know what I'm doing wrong?
>
> Thanks
> Andre
> 
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> *Gesendet:* Dienstag, 3. Februar 2015 20:39
> *An:* freesurfer@nmr.mgh.harvard.edu
> *Betreff:* Re: [Freesurfer] tksurfer
>
>
> Is it world readable? You might also change its name to license.txt
>
>
> On 2/3/15 12:13 PM, André Schmidt wrote:
>> Dear experts,
>>
>> I like to see the obtained annotation files using tksurfer. However, I
>> already got the following error message if I use tksurfer HC001 lh
>> inflated in the terminal:
>>
>> FreeSurfer license file /Applications/freesurfer/.license not found
>>
>> But there is a .license file in that folder.
>>
>> Can you help me to solve this problem?
>>
>> Thank you very much
>> Andre
>>
>>
>> ___
>> 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
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] tksurfer

[André Schmidt]

Thank you.

I've changed the file to license.txt (see attached) and tried "chmod -R a+x 
/Applications/freesurfer/license" from the terminal, but got the message 
"chmod: Unable to change file mode on /Applications/freesurfer/license: 
Operation not permitted".

Do you know what I'm doing wrong?

Thanks
Andre

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Gesendet: Dienstag, 3. Februar 2015 20:39
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] tksurfer


Is it world readable? You might also change its name to license.txt


On 2/3/15 12:13 PM, André Schmidt wrote:
Dear experts,

I like to see the obtained annotation files using tksurfer. However, I already 
got the following error message if I use tksurfer HC001 lh inflated in the 
terminal:

FreeSurfer license file /Applications/freesurfer/.license not found

But there is a .license file in that folder.

Can you help me to solve this problem?

Thank you very much
Andre



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

andre.schm...@unibas.ch
19410
 *ChTS8AxE6Mbk
___
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] Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2

[pradeep mahato]

Hi Roberto,

I had the same problem, you need to re run the recon process using
recon-all -s   -cortribbon.

Hope it helps

Pradeep.

On Fri, Feb 6, 2015 at 6:37 PM, Roberto Medeiros de Souza <
roberto.medeiros.so...@gmail.com> wrote:

> Hi,
> I'm knew to FreeSurfer. I am using the stable v5.3 and I am having the
> known issue about
> "Creation of the aseg.stats table fails when only running -autorecon1 or
> -autorecon2 because ribbon.mgz is not present." The FreeSurfer page (
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) says that this
> problem has been solved and that I should ask for a patch. Does anyone
> knows where I can get this patch?
>
>
> Thanks in advance!
>
> Roberto Medeiros de Souza
>
>
> ___
> 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.
>
>


-- 
Pradeep Kumar Mahato
___
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] Labeling of preSMA?

[Bruce Fischl]

Hi Silas

as far as I know there isn't a presma label. I'm also not sure how well 
thresholding based  on y will do either.

sorry
Bruce



On Fri, 6 Feb 2015, Silas wrote:

> Hi Freesurfer team,
> 
> I'm currently investigating the volume of preSMA. Is there an existing label
> of preSMA?
> 
> If not, together preSMA and SMA is also known as Brodmann Area 6, which is
> labeled already. PreSMA is located just rostrally to SMA in BA6, and i was
> wondering if it is possible to distinguish between preSMA and SMA by making
> a limit in y=0?
> 
> Thanks,
> 
> Best, Silas
> 
>
___
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] Freesurfer could not accurately recognize the voxel size

[Bruce Fischl]

Hi Yawu

what was the full recon-all command line? What is your input format? If 
all else fails you can mri_convert your input volume nifti or mgz and 
override what is in the header (e.g. mri_convert -iks 1 ...)

cheers
Bruce
On Fri, 6 Feb 
2015, Liu Y wrote:

> Dear Experts,
> When I run recon-all -cw256 -s problemcase -all, the program seems not able
> accurately to recognize the voxel size in this problematic case, in other
> cases there is no problem. The program gave a warning like this:
> 
> WARNING===
> ==
> The physical sizes are (240.00 mm, 240.00 mm, 338.00 mm), which cannot fit
> in 256^3 mm^3 volume.
> The resulting volume will have 338 slices.
> If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).
> ===
> ==
> 
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz...
> TR=8.08, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0, -1, 0)
> j_ras = (0, 0, 1)
> k_ras = (1, 0, 0)
> Original Data has (1, 1, 2) mm size and (240, 240, 169) voxels.
> Data is conformed to 1 mm size and 338 voxels for all directions
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz...
> 
> 
> ERROR! FOV=338.000 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> 
> 
> Then I checked the orig.mgz, the image was re-scaled (stretched) in
> left-right direction, and could not see the left and right boundaries of the
> brain. The program said that the Original Data has (1, 1, 2) mm size, but
> actually the voxel size is 1*1*1 mm3.
> 
> The freesurfer version 5.3, Ubuntu 12.04
> 
> Thanks,
> 
> Yawu
> 
> 
> 
>
___
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] Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2

[Roberto Medeiros de Souza]

Hi,
I'm knew to FreeSurfer. I am using the stable v5.3 and I am having the
known issue about
"Creation of the aseg.stats table fails when only running -autorecon1 or
-autorecon2 because ribbon.mgz is not present." The FreeSurfer page (
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) says that this
problem has been solved and that I should ask for a patch. Does anyone
knows where I can get this patch?


Thanks in advance!

Roberto Medeiros de Souza
___
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] Problems with quantitative T1 images and Freeview

[Pernille Iversen]

​
 g466_qMRI_R1.nii.gz

​Dear Ruopeng,
I just had to make sure about data rights issues before sending you the
image. No problem there.

I have attached the nifti file that I used. There were some attachment size
issues, please let me know if you cannot access the file.

Thank you for looking into this!

Kind regards,
Pernille

On Mon, Feb 2, 2015 at 3:47 PM, Ruopeng Wang 
wrote:

> Would it be possible to send us an image file that you had problem with?
>
> Best,
> Ruopeng
>
> On Feb 2, 2015, at 7:38 AM, Pernille Iversen  wrote:
>
> > Dear Freesurfer team,
> > We calculate our T1 images from quantitative sequences. I have tried to
> process one of these images with the FS pipeline and it finishes apparently
> without errors. However, when I try to load any of the .mgz files in
> Freeview, the images appears as a white box. Changing the slider settings
> for opacity, window, level, min or max does not help. The only way I can
> get a hint of a brain (including a lot of noise) is to change color map to
> colorlut, so maybe Freeview has problems with showing these images.
> >
> > Any suggestions how to proceed? Are there any special settings I need
> for the image generation?
> >
> > Thanks in advance.
> >
> > Pernille
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Pernille Iversen, PhD
Manager of Reader Centre
Danish Research Centre for Magnetic resonance
Center for Functional and Diagnostic Imaging and Research
MR-department, 714
Kettegaard Allé 30 tel: 00 45 3862 6205
Hvidovre Hospital  fax: 00 45 3862 1620
2650 Hvidovre   mail:  pern...@drcmr.dk
Denmarkwww:  www.drcmr.dk/
www.cimbi.dk
___
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] Labeling of preSMA?

[Silas]

Hi Freesurfer team,

I'm currently investigating the volume of preSMA. Is there an existing label of 
preSMA?

If not, together preSMA and SMA is also known as Brodmann Area 6, which is 
labeled already. PreSMA is located just rostrally to SMA in BA6, and i was 
wondering if it is possible to distinguish between preSMA and SMA by making a 
limit in y=0?

Thanks,

Best, Silas
  ___
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] V1 masking

[David Soto]

Hi,

I have been succesfully using mri_label2vol on the V1.labels to get a nii
file
(i.e. mri_label2vol --label rh.V1.label  --temp
$SUBJECTS_DIR/$i/mri/orig/001 --identity --o rV1.nii --subject $i --hemi rh
--proj frac 0 1 0.01)


but now I would like to use the "v1.prob.label" to get a .nii file that
 includes the probabilities of a voxel being on V1.

is this possible?

many thanks!
david
___
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.