[Freesurfer] mri_glmfit-sim with pre-cached fails

[Ed Gronenschild]

Hi,

I want to apply a cluster correction with mri_glmfit-sim with
the --cache option:

mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs

It fails with the error message that it can't find the file:

FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc- 
z.csd

(FSDir is the directory where FreeSurfer is located,
version 5.0.0, Mac OSX10.5)

Looking at the content of the fsaverage/lh/cortex directory
than indeed, only the directories fwhm01, fwhm02, ..., fwhm30
are present.

In the log file from mri_glmfit I can read that the residualFWHM
is 34.005014. Since this FWHM is automatically derived by
mri_glmfit, does it mean that I can never use the --cache option
in this case?

Cheers,
Ed


___
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] help about the testing Freesurfer

[yawu Liu]

Hi Experts,
I have baseline and followup MRI data,   when I run"recon-all -s AndiS \
   -i /home/d4201z/Desktop/fs/1/18991230_00anonymouss002a1001.nii

 
   -i /home/d4201z/Desktop/fs/2/18991230_00anonymouss004a1001.nii"
 
Only the first dataset(baseline) were processed with out any problem, but it 
stops at "d4201z-CELSIUS-M470-2:~> 
-i /home/d4201z/Desktop/fs/2/18991230_00anonymouss004a1001.nii"
, When I click return key, the software says -i could not found.

Could you give me hints on how to fix the problem? 

 
  ___
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] help about the testing Freesurfer

[Bruce Fischl]

You need a \ at the end of the 2nd line
Cheers
Bruce



On Sep 27, 2012, at 7:42 AM, yawu Liu  wrote:

> Hi Experts,
> I have baseline and followup MRI data,   when I run
> "recon-all -s AndiS \
>-i /home/d4201z/Desktop/fs/1/18991230_00anonymouss002a1001.nii
> 
>  
>-i /home/d4201z/Desktop/fs/2/18991230_00anonymouss004a1001.nii"
>  
> Only the first dataset(baseline) were processed with out any problem, but it 
> stops at "d4201z-CELSIUS-M470-2:~> 
> -i /home/d4201z/Desktop/fs/2/18991230_00anonymouss004a1001.nii"
> , When I click return key, the software says -i could not found.
> 
> Could you give me hints on how to fix the problem? 
> 
>  
> ___
> 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] Longitudinal processing

[Allison Gruber]

Hello,

I am using the longitudinal processing stream to analyze a data set. I  
have two questions:

1: We are expecting there to be significant changes in the volume of  
certain structures and gray matter between time point 1 and 2. We  
wanted to make sure the longitudinal stream is still appropriate.

2: If some subjects do not have both time points, should we process  
them as individual time points or should we use a template brain in  
order to use the longitudinal stream?

Thank you very much,
Allison

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


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

Re: [Freesurfer] mri_glmfit-sim with pre-cached fails

[Douglas N Greve]

Hi Ed, when I created the cache, I only went up to 30mm FWHM thinking 
that no one would ever go above it, or maybe should never go above it. I 
can create tables at higher smoothing levels, but 34mm is a lot of 
smoothing. How much did you apply to the data?
doug

On 09/27/2012 05:48 AM, Ed Gronenschild wrote:
> Hi,
>
> I want to apply a cluster correction with mri_glmfit-sim with
> the --cache option:
>
> mri_glmfit-sim --glmdir my_glmdir --cache 1.3 abs
>
> It fails with the error message that it can't find the file:
>
> FSDir/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th1.3/mc-
> z.csd
>
> (FSDir is the directory where FreeSurfer is located,
> version 5.0.0, Mac OSX10.5)
>
> Looking at the content of the fsaverage/lh/cortex directory
> than indeed, only the directories fwhm01, fwhm02, ..., fwhm30
> are present.
>
> In the log file from mri_glmfit I can read that the residualFWHM
> is 34.005014. Since this FWHM is automatically derived by
> mri_glmfit, does it mean that I can never use the --cache option
> in this case?
>
> Cheers,
> Ed
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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] FreeSurfer Skull Strip issue and longitudinal runs

[Rashmi Singh]

Hello FreeSurfer expets,
 Our study requires our subjects to be scanned 3-4 times and then I use
FreeSurfer Tool to generate their voulumetrics. Since I do several time
points on a subjects  also perform the longitudinal runs and then take the
volumetrics information from longitudinal run output for each time point
subject wise.
 To do the ccros sectional time point runs I performed run recon all on my
subjects T1 Mparge data as follows:
recon-all -s SUBjid -use-mritotal -all  outFSSubjid &

I examined the output data for skull stripping and I am finding errors.
What do you suggest: shall I try to correct the skull stripping on the
cross sectional out put before performing the base and longitudinal run or
shall I complete all the runs and do skull strip editing in the output of
the longitudinal run data.
Please advise.
Thanks,
Rashmi.


I am 

On 3/2/12 8:02 AM, "Bruce Fischl"  wrote:

>Hi Rashmi
>
>what version of FS are you using? And what sequence are you using? There
>will of course be noise-induced variation across scans, which in the best
>case is around 2%. But that only occurs if you use multi-echo (high
>bandwidth sequence) and are careful about subject positioning to minimize
>differential gradient nonlinearity distortions.  You should also make
>sure 
>that your outlier measurements aren't significantly more motion corrupted
>than your other scans. Finally, it can also help to control for hydration
>status and time-of-day.
>
>cheers
>Bruce
>
>
>
>On Thu, 1 Mar 2012, Rashmi Singh wrote:
>
>> Hello,
>>  I am finding differences  in hippocampus  voulme of same subject when
>>scanned at different times . Our study requires our subjects to be
>>scanned 3-4 times (T0-T3)  within a
>> period of 1 month. We have performed MRI Scanning on all our subjects
>>with same sequence using 3T GE scanner.
>> Please suggest the reason behind this difference and how would I go
>>about correcting it.
>> For example following are the hippocampal  values for two subjects ( A
>>and AA ) calculated by freesurfer from different scans. Surprisingly
>>for these two subjects T3 and T2
>> Hipp-values  for A and AA respectively that are differing from the
>>other timepoints  are  same.
>> 
>> Left-Hippocampus
>>   Right-Hippocampus
>> A.T0
>> 3537
>> 3632
>> A.T1
>> 3629
>> 3796
>> A.T2
>> 3536
>> 3782
>> A.T3
>> 3096
>> 3671
>> AA.T1
>> 4245
>> 4667
>> AA.T2
>> 3096
>> 3671
>> AA.T3
>> 4341
>> 4491
>> 
>> 
>>_
>>_
>>__
>> 
>> This document may contain information covered under the Privacy Act, 5
>>USC 552(a), and/or the Health Insurance Portability and Accountability
>>Act (PL 104-191) and its various
>> implementing regulations and must be protected in accordance with those
>>provisions. Healthcare information is personal and sensitive and must be
>>treated accordingly. If this
>> correspondence contains healthcare information it is being provided to
>>you after appropriate authorization from the patient or under
>>circumstances that don't require patient
>> authorization. You, the recipient, are obligated to maintain it in a
>>safe, secure and confidential manner. Redisclosure without additional
>>patient consent or as permitted by
>> law is prohibited. Unauthorized redisclosure or failure to maintain
>>confidentiality subjects you to application of appropriate sanction. If
>>you have received this
>> correspondence in error, please notify the sender at once and destroy
>>any copies you have made.
>> 
>>
>
>
>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

Re: [Freesurfer] DTI Spatial Normalization

[Ali Ezzati]

Hello,

I am new to DTI analysis and I am trying to follow up the manual. I have 2 
questions:

1) I cannot find any data related to CVS space in the $FREESURFER_HOME/subjects
Can you please help me find or get  the "cvs_avg35/mri/norm.mgz"? Currently, I 
am using FreeSurfure 5.1 on Linux, is CVS space available for the latest 
version?

2) How should I change these commands to use MNI space instead of CVS?
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \
--mov $SUBJECTS_DIR/$subj/dtrecon/fa-masked.mgz \
--o $SUBJECTS_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg

Thank you for your help.
Ali Ezzati
___
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] [TRACULA] trac-preproc error while reruning with an 'init=1' option

[Anastasia Yendiki]

Hi Juke - I apologize for the late response. I was away and I'm still 
catching up on email.


It looks like it fails while it's loading the atlas data (here the 4th out 
of 33 atlas subjects). Does this happen in other cases? Are the cases that 
fail running on a machine with less memory than the cases that don't?


a.y

PS: I'm assuming you mean "reinit=1".

On Tue, 11 Sep 2012, Juke Cha wrote:


Hi Anastasia,

After an intial tracula pipeline procedure, I found some tracts were not 
successfully
reconstructed. Their aparc+aseg looked fine to me. So I reran the trac-preproc 
-prior
and trac-path with an option, 'init=1' in a dmrirc file.

 Now, the analysis's running well on some, but not the other. I've got an error 
in
trac-preproc -prior:

INFO: Rejected 536 streamlines for straying off mask
INFO: Rejected 36 streamlines for reversing direction
INFO: Rejected 0 streamlines as length outliers
INFO: Have 4722 total streamlines (min/mean/max length: 8/57/104)
Loading list of excluded streamlines from
/home/brain/F/JOSH/fs/1006/dlabel/mni/lh.unc_AS_avg33_mni_flt_cpts_all.bad.txt
INFO: Found 3 streamlines to be excluded
Loading segmentation from
/usr/local/freesurfer//trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from
/usr/local/freesurfer//trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from
/usr/local/freesurfer//trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from
/usr/local/freesurfer//trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from
/usr/local/freesurfer//trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from
/usr/local/freesurfer//trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz
Loading segmentation from
/usr/local/freesurfer//trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz
Loading cortex mask from
/usr/local/freesurfer//trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz

trac-preproc exited with ERRORS at Tue Sep 11 11:03:52 EDT 2012



What would cause this and how can I fix this? Thanks for your help in advance.


-Jiook


___
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] long_mris_slopes command: temporal average calculation

[Martin Reuter]

Hi Shannon,

long_mris_slopes works for surface maps (both thickness and volume
should work). In both cases it should compute the temporal average. 

I have another scripts that works for stats files (long_stats_slopes) in
the same way.

How many time points do you have, how far apart (equally spaced?).

Best, Martin

On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote:
> Hi Martin,
>When I used the long_mris_slopes  command for the thickness, the
> average thickness calculated in FreeSurfer was pretty similar to
> averaging the values in FreeSurfer. Does this command only work
> thickness measures and not for volume or area? Thanks!
> 
> -Shannon 
> 
> On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter
>  wrote:
> Hi Shannon
> 
> You probably mean average thickness.
> My scripts compute the temporal average from the linear fit
> (at mid time), which can be differed from simply averaging
> values.
> Best Martin
> 
> Shannon Kogachi  wrote:
> Hi,
>  I had a question about how the temporal average is
> calculated for subjects with multiple timepoints. I
> used the long_mris_slopes command on a longitudinal
> set of data. However, when I compared the average
> volumes calculated through this command to the average
> volumes calculated in excel after extracting the same
> vertices at the individual timepoints, these values
> did not match up. The average volumes calculated
> through long_mris_slopes were smaller. Please let me
> know if there is a way to explain this discrepancy.
> Thank you!
> 
> -Shannon K.
> 
> 
> 
> __
> 
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Sent from my phone, please excuse brevity.
> 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.
> 
> 
> 
> 
> 
> -- 
> Shannon Kogachi
> Clinical Research Coordinator
> 
> Neuroscience and MRI Research Program
> Department of Medicine
> JABSOM, University of Hawaii
> 1356 Lusitana Street, 7th Floor
> Honolulu, HI 96813
> (808) 691 - 8763


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

Re: [Freesurfer] [TRACULA] short thin tracks

[Anastasia Yendiki]

Hi Akvile - Sorry for the late response, I was out of town for a bit.

At first glance it looks like all the tracts are stuck where they're 
initialized. This might happen occasionally for a tract if initializing it 
is tricky (i.e., if the subject is not well aligned to the atlas, if the 
brain mask has a hole, etc), which is why the reinit option exists. But 
I've never seen it happen to all tracts, so something's fishy here.


If you upload all the tracula-related directories for this subject (dmri, 
dlabel, dpath, scripts), I'll take a look.


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

a.y

On Thu, 13 Sep 2012, Akvile Lukose wrote:



Hello Freesurfers, 

I ran into a problem running TRACULA that I couldn't solve myself, and I would 
really
appreciate if you could have a look. 

I am running a FS 5.1 on mac os x 10.7.4 (intel 64bit) machine with 16GB RAM. 

I extracted the bvals and bvecs with the dcm2nii converter and adjusted the 
format to
what FS expects (scans acquired on a non-Siemens scanner). 

I attach the dmrirc file as well. 

First, I had a memory problem (cannot alloc memory) during the –prep stage. The 
new
compiled update from here 
(http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula )helped
and –prep stage finished without any errors. 

I was not able to run bedpostx from dmrirc configuration file. I could work 
around it
by running bedpostx directly on dmri directory (as described
here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html). 
Then
I had a problem with symlinks, I created them manually and after that  it worked
fine, I had all the output files as listed here
(http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html). 

-path worked also without any errors, but I keep getting very short thin tracks 
(all
tracks) (snapshot attached). There is nothing wrong with the  aparc+aseg.mgz. I 
tried
rerunning every stage after I added option "set reinit=1" (as described
here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21990.html), 
but
unfortunately it didn't help.

Do you have any ideas how to fix it? Thank you very much in advance! 

Kind regards,

Akvile Lukose


___
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] Longitudinal processing

[Martin Reuter]

Hi Allison,

with very large changes across time, the longitudinal stream can fail or
may need more manual intervention (edits). We have run it successfully
on Huntington's Disease patients with large changes and many time
points. The only way to find out if it works on your data is to run it.

I have recently made changes to the longitudinal stream (to be available
in FS 5.2) that will allow inclusion of subject with a single time
point. Currently we recommend to exclude them instead of running them as
individual time points. The reason is that results in those cross
sectional runs will be different from longitudinal runs and this may
introduce a bias (especially if single time points subjects are more
likely from one group than the other). 

Best, Martin


On Thu, 2012-09-27 at 10:51 -0400, Allison Gruber wrote:
> Hello,
> 
> I am using the longitudinal processing stream to analyze a data set. I  
> have two questions:
> 
> 1: We are expecting there to be significant changes in the volume of  
> certain structures and gray matter between time point 1 and 2. We  
> wanted to make sure the longitudinal stream is still appropriate.
> 
> 2: If some subjects do not have both time points, should we process  
> them as individual time points or should we use a template brain in  
> order to use the longitudinal stream?
> 
> Thank you very much,
> Allison
> 
> ___
> 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] message bouncing

[Rashmi Singh]

Well,
 Correct me if I am doing something wrong while posting my emails.
Whenever I post my emails to freesurfer-requ...@nmr.mgh.harvard.edu my
emails bounces.
So today I emailed my post to Bruce's email,
freesurfer@nmr.mgh.harvard.edu and freesurfer-requ...@nmr.mgh.harvard.edu.
I got a bounce reply from the freesurfer-requ...@nmr.mgh.harvard.edu email.

So let me know what am doing wrong?
Rashmi

On 9/27/12 11:52 AM, "Help Desk Elf --- Chris Johnson"
 wrote:

>  Rashmi,
>
>  I'm seeing an archive of a post from today at 12:04:28 EDT 2012.
>Are you still having trouble?  You are definitely still on the list.
>
>> I see. Nick and/or help: can you investigate?
>>
>> thanks
>> Bruce
>>
>>
>> On Thu, 27 Sep 2012, Rashmi Singh wrote:
>>
>>>  Reply,
>>>  Yes I started posting since last year, but suddenly after July this
>>>year
>>>  my posts have started bouncing back.
>>>  That is why I finally emailed my issue to your personal id today.
>>>  Thank you !
>>>  Rashmi.
>>> 
>>>
>>>  On 9/27/12 11:31 AM, "Bruce Fischl" 
>>>wrote:
>>> 
>>> >  Hi Rashmi
>>> > 
>>> >  are you a member of the list?
>>> > 
>>> >  Bruce
>>> > 
>>> >  On Thu, 27 Sep 2012, Rashmi Singh wrote:
>>> > 
>>> > >  Hello Bruce,
>>> > >  I am somehow unable to send message to the Freesurfer request
>>>board.
>>> > >  All my
>>> > >  e mails are bouncing.
>>> > >  Please advise.
>>> > >  Rashmi
>>> > > 
>>> > > 
>>> > 
>>> > 
>>> >  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.
>>> > 
>>> 
>>> 
>>> 
>>> 
>>
>>
>>
>>
>
>-- Chris Johnson (http://help.nmr.mgh.harvard.edu)
>
>--
>-
>Chris Johnson   |Internet: john...@nmr.mgh.harvard.edu
>Systems Administrator   |Web:
>http://www.nmr.mgh.harvard.edu/~johnson
>NMR Center  |Voice:617.726.0949
>Mass. General Hospital  |FAX:  617.726.7422
>149 (2301) 13th Street  |"Life.  Don't talk to me about life."
>Marvin the
>Charlestown, MA., 02129 USA | Paranoid Android
>--
>-


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

Re: [Freesurfer] TRACULA - failed corpus callosum forceps major

[Anastasia Yendiki]

Hi Clare - Sorry for responding late to any email that was sent while I 
was away.


The fmajor and slft are sometimes tricky in their initialization b/c of 
their high curvature. The initial guess for the path is chosen from the 
atlas and if it's not well-aligned and veers off the subject's white 
matter somewhere the initialization will fail. In those cases the 
path.pd.nii.gz will contain only the initial path, so you can overlay it 
on the subject's FA map and see if that's what's happening.


If you try the reinit trick a few times (if you keep doing it, it'll try 
different initializations each time) and it doesn't work, you can also try 
increasing the number of controls points (say, set ncpts = 7) for these 
cases.


If none of this works, I can try to take a look at one of these data sets.

Hope this helps,
a.y

On Fri, 14 Sep 2012, Gibbard, Clare wrote:


Hello,

I have tried out running TRACULA on 20 subjects.  It all seemed to work well 
except
that in 8 of the subjects the corpus callosum forceps major was either missing 
or was
a very small cluster.  The same happened for the temporal SLF of 2 subjects.

I read previous posts related to this and tried re-running the affected 
subjects with
set reinit =1.  However, the results were very similar to before.  I have 
checked the
registrations and they are not perfect, but not wildly inaccurate.

Are you able to suggest any options for me to try?  I have attached the dmrirc 
file I
used for the first run (called dmrirc-original) as well as the one for 
re-running the
subjects whose CC was not segmented (called dmrirc).

Thank you.

Best wishes,
Clare

___
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] TRACULA Question

[Anastasia Yendiki]

Hi Gabor - Tracula doesn't use the BA labels, only the labels in the 
aparc+aseg. I hope this answers your question.

a.y

On Sun, 16 Sep 2012, Gabor Perlaki wrote:

> Dear Anastasia,
>
> Earlier I was posted an issue about BA44/pars triangular:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html
>
> Because TRACULA also uses the cortical parcellation it may be
> important to handle this issue somehow. Is it handled in TRACULA
> analysis? Does it affect the result of WM-volumes?
>
> Thank you for your answer,
> Gabor
> ___
> 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] message bouncing

[Louis Nicholas Vinke]

Hi Rashmi,
When posting questions to the list, send them only to 
freesurfer@nmr.mgh.harvard.edu.  Your email address is still subscribed 
and is not blocked from posting to the FS list.
-Louis

On Thu, 27 Sep 2012, Rashmi Singh wrote:

> Well,
> Correct me if I am doing something wrong while posting my emails.
> Whenever I post my emails to freesurfer-requ...@nmr.mgh.harvard.edu my
> emails bounces.
> So today I emailed my post to Bruce's email,
> freesurfer@nmr.mgh.harvard.edu and freesurfer-requ...@nmr.mgh.harvard.edu.
> I got a bounce reply from the freesurfer-requ...@nmr.mgh.harvard.edu email.
>
> So let me know what am doing wrong?
> Rashmi
>
> On 9/27/12 11:52 AM, "Help Desk Elf --- Chris Johnson"
>  wrote:
>
>>  Rashmi,
>>
>>  I'm seeing an archive of a post from today at 12:04:28 EDT 2012.
>> Are you still having trouble?  You are definitely still on the list.
>>
>>> I see. Nick and/or help: can you investigate?
>>>
>>> thanks
>>> Bruce
>>>
>>>
>>> On Thu, 27 Sep 2012, Rashmi Singh wrote:
>>>
  Reply,
  Yes I started posting since last year, but suddenly after July this
 year
  my posts have started bouncing back.
  That is why I finally emailed my issue to your personal id today.
  Thank you !
  Rashmi.


  On 9/27/12 11:31 AM, "Bruce Fischl" 
 wrote:

>  Hi Rashmi
>
>  are you a member of the list?
>
>  Bruce
>
>  On Thu, 27 Sep 2012, Rashmi Singh wrote:
>
>>  Hello Bruce,
>>  I am somehow unable to send message to the Freesurfer request
 board.
>>  All my
>>  e mails are bouncing.
>>  Please advise.
>>  Rashmi
>>
>>
>
>
>  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.
>




>>>
>>>
>>>
>>>
>>
>> -- Chris Johnson (http://help.nmr.mgh.harvard.edu)
>>
>> --
>> -
>> Chris Johnson   |Internet: john...@nmr.mgh.harvard.edu
>> Systems Administrator   |Web:
>> http://www.nmr.mgh.harvard.edu/~johnson
>> NMR Center  |Voice:617.726.0949
>> Mass. General Hospital  |FAX:  617.726.7422
>> 149 (2301) 13th Street  |"Life.  Don't talk to me about life."
>> Marvin the
>> Charlestown, MA., 02129 USA | Paranoid Android
>> --
>> -
>
>
> ___
> 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

Re: [Freesurfer] FreeSurfer Skull Strip issue and longitudinal runs

[Martin Reuter]

Hi Rashimi,

please read
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits 
it should explain everything.

The clean way would be to edit the brainmask in the cross sectional
runs, complete them, run the base and the longs. Optimally no edits
should be necessary in the base and longs if cross are correct.

A potential short cut (depending on how bad the skull strips are) would
be to run cross and base, then edit only the base. This can work if the
skull strip is not too bad and if the asegs in the cross are good.

Best, Martin.

On Thu, 2012-09-27 at 16:04 +, Rashmi Singh wrote:
> Hello FreeSurfer expets,
>  Our study requires our subjects to be scanned 3-4 times and then I use
> FreeSurfer Tool to generate their voulumetrics. Since I do several time
> points on a subjects  also perform the longitudinal runs and then take the
> volumetrics information from longitudinal run output for each time point
> subject wise.
>  To do the ccros sectional time point runs I performed run recon all on my
> subjects T1 Mparge data as follows:
> recon-all -s SUBjid -use-mritotal -all  outFSSubjid &
> 
> I examined the output data for skull stripping and I am finding errors.
> What do you suggest: shall I try to correct the skull stripping on the
> cross sectional out put before performing the base and longitudinal run or
> shall I complete all the runs and do skull strip editing in the output of
> the longitudinal run data.
> Please advise.
> Thanks,
> Rashmi.
> 
> 
> I am 
> 
> On 3/2/12 8:02 AM, "Bruce Fischl"  wrote:
> 
> >Hi Rashmi
> >
> >what version of FS are you using? And what sequence are you using? There
> >will of course be noise-induced variation across scans, which in the best
> >case is around 2%. But that only occurs if you use multi-echo (high
> >bandwidth sequence) and are careful about subject positioning to minimize
> >differential gradient nonlinearity distortions.  You should also make
> >sure 
> >that your outlier measurements aren't significantly more motion corrupted
> >than your other scans. Finally, it can also help to control for hydration
> >status and time-of-day.
> >
> >cheers
> >Bruce
> >
> >
> >
> >On Thu, 1 Mar 2012, Rashmi Singh wrote:
> >
> >> Hello,
> >>  I am finding differences  in hippocampus  voulme of same subject when
> >>scanned at different times . Our study requires our subjects to be
> >>scanned 3-4 times (T0-T3)  within a
> >> period of 1 month. We have performed MRI Scanning on all our subjects
> >>with same sequence using 3T GE scanner.
> >> Please suggest the reason behind this difference and how would I go
> >>about correcting it.
> >> For example following are the hippocampal  values for two subjects ( A
> >>and AA ) calculated by freesurfer from different scans. Surprisingly
> >>for these two subjects T3 and T2
> >> Hipp-values  for A and AA respectively that are differing from the
> >>other timepoints  are  same.
> >> 
> >> Left-Hippocampus
> >>   Right-Hippocampus
> >> A.T0
> >> 3537
> >> 3632
> >> A.T1
> >> 3629
> >> 3796
> >> A.T2
> >> 3536
> >> 3782
> >> A.T3
> >> 3096
> >> 3671
> >> AA.T1
> >> 4245
> >> 4667
> >> AA.T2
> >> 3096
> >> 3671
> >> AA.T3
> >> 4341
> >> 4491
> >> 
> >> 
> >>_
> >>_
> >>__
> >> 
> >> This document may contain information covered under the Privacy Act, 5
> >>USC 552(a), and/or the Health Insurance Portability and Accountability
> >>Act (PL 104-191) and its various
> >> implementing regulations and must be protected in accordance with those
> >>provisions. Healthcare information is personal and sensitive and must be
> >>treated accordingly. If this
> >> correspondence contains healthcare information it is being provided to
> >>you after appropriate authorization from the patient or under
> >>circumstances that don't require patient
> >> authorization. You, the recipient, are obligated to maintain it in a
> >>safe, secure and confidential manner. Redisclosure without additional
> >>patient consent or as permitted by
> >> law is prohibited. Unauthorized redisclosure or failure to maintain
> >>confidentiality subjects you to application of appropriate sanction. If
> >>you have received this
> >> correspondence in error, please notify the sender at once and destroy
> >>any copies you have made.
> >> 
> >>
> >
> >
> >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

Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries

[Anastasia Yendiki]

Hi Joy - How were your bvecs and bvals files generated? In the past some 
people have had problems with files exported from Excel b/c it generates 
text files with Windows-specific end-of-line characters that cannot be 
read properly on Linux. Do the files look normal when you run "more" on 
them on the system where you ran trac-all?

a.y

On Wed, 26 Sep 2012, Loi wrote:

> Dear FreeSurfers,
>
> I am trying to run trac-all -prep on a single subject, and get the
> following error:
>
> dtifit -k 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz
> -m 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz
> -r 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs
> -b 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals
> -o 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit
> Error: bvecs and bvals don't have the same number of entries
>
> I have searched the message thread, and cannot seem to find a solution
> applicable to my situation: it seems that the trac-all process
> generates transposed bvec and bval files.
> Therefore, I tried transposing these manually and specifying the
> location to these files (as explained in the tutorial:
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but
> attempting to run trac-all again still leads to the same result: new
> bval and bvec files are generated, and I receive the same error
> message.
>
> Does anyone know how I can solve this problem?
>
> Thank you,
> Joy-Loi
>
>
> *
> My configuration file:
>
>
> setenv SUBJECTS_DIR
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
>
> set dtroot = 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
>
> set subjlist = id101
> set runlist = 1
>
> set dcmroot = 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
> set dcmlist = id101/orig/1.dcm
>
> set bvalfile = 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt
>
> set bvecfile = 
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt
>
> set nb0 = 10
>
> set doeddy = 1
> set dorotbvecs = 1
> set thrbet = 0.3
> set doregflt = 1
> set doregbbr = 0
> set doregmni = 1
> set mnitemp =  /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
>
> #set trainfile =
> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt
>
> set pathlist = (lh.cst_AS rh.cst_AS \
>lh.ilf_AS rh.ilf_AS \
> lh.unc_AS rh.unc_AS \
>fmajor_PP fminor_PP \
>lh.atr_PP rh.atr_PP \
>lh.cab_PP rh.cab_PP \
>lh.ccg_PP rh.ccg_PP \
>lh.slfp_PP rh.slfp_PP \
>lh.slft_PP rh.slft_PP)
>
>
> set ncpts = 5
>
> set usetrunc = 1
>
>
>
>
>
> *
> My bvals:
>
> 0.00
> 0.00
> 0.00
> 0.00
> 0.00
> 0.00
> 0.00
> 0.00
> 0.00
> 0.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
> 700.00
>
> *
> My bvecs:
>
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> 0.000 0.000 0.000
> -0.9998760 0.0011040 0.0157340
> -0.7705615 0.6320276 0.0823114
> -0.2461791 0.0273479 0.9688392
> -0.7953558 0.1076421 0.5965091
> 0.4620816 -0.8755928 0.1407778
> 0.2261090 -0.8553081 -0.4661796
> 0.2601186 0.4095102 -0.8744363
> -0.7969547 -0.5877791 0.1392076
> -0.5028073 -0.5104712 0.6975709
> -0.3073035 0.1334521 -0.9422074
> 0.7957742 0.1950272 -0.5733304
> 0.8041493 0.5924478 -0.0484727
> -0.1867079 -0.9528833 0.2390659
> 0.3898569 -0.1063898 0.9147088
> 0.1341999 -0.6614532 0.7378819
> 0.3382555 0.8823941 0.3270553
> -0.7688307 -0.3139264 -0.5570900
> -0.4086013 0.6653325 0.6248017
> -0.2933309 0.7581020 -0.5824408
> 0.7689370 -0.4282441 0.4747016
> 0.1800972 0.5296402 0.8288835
> 0.7680658 0.3158178 0.5570763
> -0.2214999 0.9744585 0.0370050
> -0.4175692 -0.8418782 -0.3418731
> -0.1784475 -0.4817282 -0.8579599
> 0.3361637 0.8554551 -0.3939400
> 0.7858656 -0.5091907 -0.3509137
> 0.4194232 -0.2589429 -0.8700761
> -0.7760561 0.3511497 -0.5238622
> 0.9987836 -0.0413076 0.0269219
> __

Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries

[Loi]

Hello,

I generate the files in Linux (using gedit) and they look normal (I
have compared them to the files in the tutorial).

So far I have tried ending both with and without .txt, transposing the
files, changing to equal number of decimals and adding 'setenv LC_ALL
en_US' to the .tchsrc file.

The inputs I am using are dicoms, and even though I specify a path to
the b-value files and gradient tables I make (I originally didn't
specify these, and got the same error message), new bvecs and bvals
are generated in the trac-all -prep process, leading to the error.

Thank you,
Joy-Loi




On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki
 wrote:
>
> Hi Joy - How were your bvecs and bvals files generated? In the past some
> people have had problems with files exported from Excel b/c it generates
> text files with Windows-specific end-of-line characters that cannot be read
> properly on Linux. Do the files look normal when you run "more" on them on
> the system where you ran trac-all?
>
> a.y
>
>
> On Wed, 26 Sep 2012, Loi wrote:
>
>> Dear FreeSurfers,
>>
>> I am trying to run trac-all -prep on a single subject, and get the
>> following error:
>>
>> dtifit -k
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz
>> -m
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz
>> -r
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs
>> -b
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals
>> -o
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit
>> Error: bvecs and bvals don't have the same number of entries
>>
>> I have searched the message thread, and cannot seem to find a solution
>> applicable to my situation: it seems that the trac-all process
>> generates transposed bvec and bval files.
>> Therefore, I tried transposing these manually and specifying the
>> location to these files (as explained in the tutorial:
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but
>> attempting to run trac-all again still leads to the same result: new
>> bval and bvec files are generated, and I receive the same error
>> message.
>>
>> Does anyone know how I can solve this problem?
>>
>> Thank you,
>> Joy-Loi
>>
>>
>> *
>> My configuration file:
>>
>>
>> setenv SUBJECTS_DIR
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
>>
>> set dtroot =
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
>>
>> set subjlist = id101
>> set runlist = 1
>>
>> set dcmroot =
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
>> set dcmlist = id101/orig/1.dcm
>>
>> set bvalfile =
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt
>>
>> set bvecfile =
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt
>>
>> set nb0 = 10
>>
>> set doeddy = 1
>> set dorotbvecs = 1
>> set thrbet = 0.3
>> set doregflt = 1
>> set doregbbr = 0
>> set doregmni = 1
>> set mnitemp =  /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
>>
>> #set trainfile =
>>
>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt
>>
>> set pathlist = (lh.cst_AS rh.cst_AS \
>>  lh.ilf_AS rh.ilf_AS \
>> lh.unc_AS rh.unc_AS \
>>  fmajor_PP fminor_PP \
>>  lh.atr_PP rh.atr_PP \
>>  lh.cab_PP rh.cab_PP \
>>  lh.ccg_PP rh.ccg_PP \
>>  lh.slfp_PP rh.slfp_PP \
>>  lh.slft_PP rh.slft_PP)
>>
>>
>> set ncpts = 5
>>
>> set usetrunc = 1
>>
>>
>>
>>
>>
>> *
>> My bvals:
>>
>> 0.00
>> 0.00
>> 0.00
>> 0.00
>> 0.00
>> 0.00
>> 0.00
>> 0.00
>> 0.00
>> 0.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>> 700.00
>>
>> *
>> My bvecs:
>>
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> 0.000 0.000 0.000
>> -0.9998760 0.0011040 0.0157340
>> -0.7705615 0.6320276 0.0823114
>> -0.2461791 0.0273479 0.9688392
>> -0.7953558 0.1076421 0.5965091
>> 0.4620816 -0.8755928 0.1407778
>> 0.2261090 -0.8553081 -0.4661796
>> 0.2601186 0.4095102 -0

Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries

[Anastasia Yendiki]

Can you please send the original bvals and bvecs files (the ones that you 
specify in the configuration file), and the configuration file itself? 
Thanks!

a.y

On Thu, 27 Sep 2012, Loi wrote:

> Hello,
>
> I generate the files in Linux (using gedit) and they look normal (I
> have compared them to the files in the tutorial).
>
> So far I have tried ending both with and without .txt, transposing the
> files, changing to equal number of decimals and adding 'setenv LC_ALL
> en_US' to the .tchsrc file.
>
> The inputs I am using are dicoms, and even though I specify a path to
> the b-value files and gradient tables I make (I originally didn't
> specify these, and got the same error message), new bvecs and bvals
> are generated in the trac-all -prep process, leading to the error.
>
> Thank you,
> Joy-Loi
>
>
>
>
> On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki
>  wrote:
>>
>> Hi Joy - How were your bvecs and bvals files generated? In the past some
>> people have had problems with files exported from Excel b/c it generates
>> text files with Windows-specific end-of-line characters that cannot be read
>> properly on Linux. Do the files look normal when you run "more" on them on
>> the system where you ran trac-all?
>>
>> a.y
>>
>>
>> On Wed, 26 Sep 2012, Loi wrote:
>>
>>> Dear FreeSurfers,
>>>
>>> I am trying to run trac-all -prep on a single subject, and get the
>>> following error:
>>>
>>> dtifit -k
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz
>>> -m
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz
>>> -r
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs
>>> -b
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals
>>> -o
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit
>>> Error: bvecs and bvals don't have the same number of entries
>>>
>>> I have searched the message thread, and cannot seem to find a solution
>>> applicable to my situation: it seems that the trac-all process
>>> generates transposed bvec and bval files.
>>> Therefore, I tried transposing these manually and specifying the
>>> location to these files (as explained in the tutorial:
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but
>>> attempting to run trac-all again still leads to the same result: new
>>> bval and bvec files are generated, and I receive the same error
>>> message.
>>>
>>> Does anyone know how I can solve this problem?
>>>
>>> Thank you,
>>> Joy-Loi
>>>
>>>
>>> *
>>> My configuration file:
>>>
>>>
>>> setenv SUBJECTS_DIR
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
>>>
>>> set dtroot =
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
>>>
>>> set subjlist = id101
>>> set runlist = 1
>>>
>>> set dcmroot =
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
>>> set dcmlist = id101/orig/1.dcm
>>>
>>> set bvalfile =
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt
>>>
>>> set bvecfile =
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt
>>>
>>> set nb0 = 10
>>>
>>> set doeddy = 1
>>> set dorotbvecs = 1
>>> set thrbet = 0.3
>>> set doregflt = 1
>>> set doregbbr = 0
>>> set doregmni = 1
>>> set mnitemp =  /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
>>>
>>> #set trainfile =
>>>
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt
>>>
>>> set pathlist = (lh.cst_AS rh.cst_AS \
>>>  lh.ilf_AS rh.ilf_AS \
>>> lh.unc_AS rh.unc_AS \
>>>  fmajor_PP fminor_PP \
>>>  lh.atr_PP rh.atr_PP \
>>>  lh.cab_PP rh.cab_PP \
>>>  lh.ccg_PP rh.ccg_PP \
>>>  lh.slfp_PP rh.slfp_PP \
>>>  lh.slft_PP rh.slft_PP)
>>>
>>>
>>> set ncpts = 5
>>>
>>> set usetrunc = 1
>>>
>>>
>>>
>>>
>>>
>>> *
>>> My bvals:
>>>
>>> 0.00
>>> 0.00
>>> 0.00
>>> 0.00
>>> 0.00
>>> 0.00
>>> 0.00
>>> 0.00
>>> 0.00
>>> 0.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>> 700.00
>>>
>>> *
>>> My bvecs:
>>>
>>> 0.000 0.000 0.000
>>> 0.000 0.000 0.000
>>> 0.000 0.000 0.000
>>> 0.000 0.000 0.000
>>> 0.000 0.000 0.000
>>> 0.0

[Freesurfer] output problem after recon-all

[pietro de rossi]

Hi Freesurfers,

I have another quintessentially beginner's problem

I ran 5 scans through the entire pipeline (-autorecon1 -autorecon2 and
-autorecon2 -autorecon-3)

when I check the output going

tksurfer [name_of_folder_with_dcm_files] rh (or lh) inflated

and then

tkmedit [name_of_folder_with_dcm_files] norm.mgz -segmentation aseg.mgz
$FREESURFER_HOME/FreeSurferColorLUT.txt

the scans look all the sameit is like the last scan I processed was
overwritten on the previous onesdoes it make sense?

thank you very much,

Pietro

-- 
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant’Andrea
Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social and Behavioral Research
Branch, National Human Genome Research Institute (NHGRI), National
Institutes of Health (NIH), Bethesda, Maryland 20892, USA
___
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] output problem after recon-all

[Bruce Fischl]

Hi Pietro

what was your recon-all command line? You need to specify different 
subject identifiers (-s ) for the different datasets


Bruce
On 
Thu, 27 Sep 2012, pietro de rossi wrote:



Hi Freesurfers,
I have another quintessentially beginner's problem

I ran 5 scans through the entire pipeline (-autorecon1 -autorecon2 and
-autorecon2 -autorecon-3)

when I check the output going

tksurfer [name_of_folder_with_dcm_files] rh (or lh) inflated

and then

tkmedit [name_of_folder_with_dcm_files] norm.mgz -segmentation aseg.mgz
$FREESURFER_HOME/FreeSurferColorLUT.txt

the scans look all the sameit is like the last scan I processed was
overwritten on the previous onesdoes it make sense?

thank you very much,

Pietro

--
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital,
Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social and Behavioral Research
Branch, National Human Genome Research Institute (NHGRI), National
Institutes of Health (NIH), Bethesda, Maryland 20892, USA

___
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] Cerebellar volume correction

[Rachel Steinhorn]

We'd like to obtain total cerebellar volumes.  There are errors within the
cerebellar segmentation as revealed in the aseg.mgz file.  Is there a
method to manually edit the cerebellar segmentation?

Thank You,
Rachel Steinhorn
___
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] output problem after recon-all

[pietro de rossi]

sorry, I didn't realize I hadn't replied to the whole list :-)

so this

recon-all -i  -s 
-all

is the command for the whole pipeline if I understand correctly does
 represents the folder where the dcm files are?

sorry for bothering again..

2012/9/27 Bruce Fischl 

> can you cc the list on these emails? Your command line should be:
>
> recon-all -i  -s 
> -all
>
> cheers
>
> Bruce
>
>
> On Thu, 27 Sep 2012, pietro de rossi wrote:
>
>  the command line was
>>
>> recon-all -autorecon1 -autorecon2 -subjid name_of_folder_with_dcm_files
>>
>> then
>>
>> recon-all -autorecon2 -autorecon3 -subjid name_of_folder_with_dcm_files
>>
>>
>>
>> 2012/9/27 Bruce Fischl 
>>   Hi Pietro
>>
>>   what was your recon-all command line? You need to specify
>>   different subject identifiers (-s ) for the
>>   different datasets
>>
>>   Bruce
>>   On Thu, 27 Sep 2012, pietro de rossi wrote:
>>
>>   Hi Freesurfers,
>>   I have another quintessentially beginner's problem
>>
>>   I ran 5 scans through the entire pipeline (-autorecon1
>>   -autorecon2 and
>>   -autorecon2 -autorecon-3)
>>
>>   when I check the output going
>>
>>   tksurfer [name_of_folder_with_dcm_**files] rh (or lh)
>>   inflated
>>
>>   and then
>>
>>   tkmedit [name_of_folder_with_**dcm_files] norm.mgz
>>   -segmentation aseg.mgz
>>   $FREESURFER_HOME/**FreeSurferColorLUT.txt
>>
>>   the scans look all the sameit is like the last scan I
>>   processed was
>>   overwritten on the previous onesdoes it make sense?
>>
>>   thank you very much,
>>
>>   Pietro
>>
>>   --
>>   Pietro De Rossi, MD
>>   --**---
>>   Sapienza Università di Roma, Facoltà di Medicina e
>>   Psicologia, Dipartimento
>>   NESMOS (Neuroscienze, Salute Mentale, Organi di Senso),
>>   Ospedale
>>   Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
>>
>>   NESMOS Department (Neurosciences, Mental Health and
>>   Sensory Functions),
>> School of Medicine and Psychology, Sapienza University,
>> Sant?Andrea Hospital,
>> Via di Grottarossa 1035-1039, 00189 Rome, Italy
>>
>> Neurobehavioral Clinical Research Section, Social and Behavioral
>> Research
>> Branch, National Human Genome Research Institute (NHGRI),
>> National
>> Institutes of Health (NIH), Bethesda, Maryland 20892, USA
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Pietro De Rossi, MD
>> --**---
>> Sapienza Università di Roma, Facoltà di Medicina e Psicologia,
>> Dipartimento
>> NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
>> Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma
>>
>> NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
>> School of Medicine and Psychology, Sapienza University, Sant?Andrea
>> Hospital,
>> Via di Grottarossa 1035-1039, 00189 Rome, Italy
>>
>> Neurobehavioral Clinical Research Section, Social and Behavioral Research
>> Branch, National Human Genome Research Institute (NHGRI), National
>> Institutes of Health (NIH), Bethesda, Maryland 20892, USA
>>
>>


-- 
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions),
School of Medicine and Psychology, Sapienza University, Sant’Andrea
Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social and Behavioral Research
Branch, National Human Genome Research Institute (NHGRI), National
Institutes of Health (NIH), Bethesda, Maryland 20892, USA
___
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] output problem after recon-all

[Bruce Fischl]

no, it represent the name of the folder that FS will create to put the 
results of the analysis in. The -i should be the full path to one file in 
the correct (T1-weighted) dicom series
On Thu, 27 Sep 2012, pietro de rossi 
wrote:



sorry, I didn't realize I hadn't replied to the whole list :-)
so this   

recon-all -i  -s 
-all

is the command for the whole pipeline if I understand correctly does
 represents the folder where the dcm files are?

sorry for bothering again..

2012/9/27 Bruce Fischl 
  can you cc the list on these emails? Your command line should
  be:

  recon-all -i  -s
   -all

  cheers
  Bruce


  On Thu, 27 Sep 2012, pietro de rossi wrote:

the command line was

recon-all -autorecon1 -autorecon2 -subjid
name_of_folder_with_dcm_files

then

recon-all -autorecon2 -autorecon3 -subjid
name_of_folder_with_dcm_files



2012/9/27 Bruce Fischl 
      Hi Pietro

      what was your recon-all command line? You need
to specify
      different subject identifiers (-s ) for the
      different datasets

      Bruce
      On Thu, 27 Sep 2012, pietro de rossi wrote:

      Hi Freesurfers,
      I have another quintessentially beginner's
problem

      I ran 5 scans through the entire pipeline
(-autorecon1
      -autorecon2 and
      -autorecon2 -autorecon-3)

      when I check the output going

      tksurfer [name_of_folder_with_dcm_files] rh
(or lh)
      inflated

      and then

     
tkmedit [name_of_folder_with_dcm_files] norm.mgz
      -segmentation aseg.mgz
      $FREESURFER_HOME/FreeSurferColorLUT.txt

      the scans look all the sameit is like the
last scan I
      processed was
      overwritten on the previous onesdoes it
make sense?

      thank you very much,

      Pietro

      --
      Pietro De Rossi, MD
      -
      Sapienza Università di Roma, Facoltà di
Medicina e
      Psicologia, Dipartimento
      NESMOS (Neuroscienze, Salute Mentale, Organi
di Senso),
      Ospedale
      Sant'Andrea, Via di Grottarossa 1035-1039,
00189 Roma

      NESMOS Department (Neurosciences, Mental
Health and
      Sensory Functions),
School of Medicine and Psychology, Sapienza
University,
Sant?Andrea Hospital,
Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social
and Behavioral
Research
Branch, National Human Genome Research Institute
(NHGRI),
National
Institutes of Health (NIH), Bethesda, Maryland
20892, USA




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.




--
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e
Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di
Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-1039, 00189
Roma

NESMOS Department (Neurosciences, Mental Health and
Sensory Functions),
School of Medicine and Psychology, Sapienza
University, Sant?Andrea Hospital,
Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social
and Behavioral Research
Branch, National Human Genome Research Institute
(NHGRI), National
Institutes of Health (NIH), Bethesda, Maryland
20892, USA




--
Pietro De Rossi, MD
-
Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento
NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale
Sant'Andrea, Via di Grottarossa 1035-10

Re: [Freesurfer] output problem after recon-all

[pietro de rossi]

Thank you very much Bruce!
it's working.

2012/9/27 Bruce Fischl 

> no, it represent the name of the folder that FS will create to put the
> results of the analysis in. The -i should be the full path to one file in
> the correct (T1-weighted) dicom series
>
> On Thu, 27 Sep 2012, pietro de rossi wrote:
>
>  sorry, I didn't realize I hadn't replied to the whole list :-)
>> so this
>>
>> recon-all -i  -s 
>> -all
>>
>> is the command for the whole pipeline if I understand correctly does
>>  represents the folder where the dcm files are?
>>
>> sorry for bothering again..
>>
>> 2012/9/27 Bruce Fischl 
>>   can you cc the list on these emails? Your command line should
>>   be:
>>
>>   recon-all -i  -s
>>-all
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Thu, 27 Sep 2012, pietro de rossi wrote:
>>
>> the command line was
>>
>> recon-all -autorecon1 -autorecon2 -subjid
>> name_of_folder_with_dcm_files
>>
>> then
>>
>> recon-all -autorecon2 -autorecon3 -subjid
>> name_of_folder_with_dcm_files
>>
>>
>>
>> 2012/9/27 Bruce Fischl 
>>   Hi Pietro
>>
>>   what was your recon-all command line? You need
>> to specify
>>   different subject identifiers (-s > identifier>) for the
>>   different datasets
>>
>>   Bruce
>>   On Thu, 27 Sep 2012, pietro de rossi wrote:
>>
>>   Hi Freesurfers,
>>   I have another quintessentially beginner's
>> problem
>>
>>   I ran 5 scans through the entire pipeline
>> (-autorecon1
>>   -autorecon2 and
>>   -autorecon2 -autorecon-3)
>>
>>   when I check the output going
>>
>>   tksurfer [name_of_folder_with_dcm_**files] rh
>> (or lh)
>>   inflated
>>
>>   and then
>>
>>
>> tkmedit [name_of_folder_with_**dcm_files] norm.mgz
>>   -segmentation aseg.mgz
>>   $FREESURFER_HOME/**FreeSurferColorLUT.txt
>>
>>   the scans look all the sameit is like the
>> last scan I
>>   processed was
>>   overwritten on the previous onesdoes it
>> make sense?
>>
>>   thank you very much,
>>
>>   Pietro
>>
>>   --
>>   Pietro De Rossi, MD
>>   --**---
>>   Sapienza Università di Roma, Facoltà di
>> Medicina e
>>   Psicologia, Dipartimento
>>   NESMOS (Neuroscienze, Salute Mentale, Organi
>> di Senso),
>>   Ospedale
>>   Sant'Andrea, Via di Grottarossa 1035-1039,
>> 00189 Roma
>>
>>   NESMOS Department (Neurosciences, Mental
>> Health and
>>   Sensory Functions),
>> School of Medicine and Psychology, Sapienza
>> University,
>> Sant?Andrea Hospital,
>> Via di Grottarossa 1035-1039, 00189 Rome, Italy
>>
>> Neurobehavioral Clinical Research Section, Social
>> and Behavioral
>> Research
>> Branch, National Human Genome Research Institute
>> (NHGRI),
>> National
>> Institutes of Health (NIH), Bethesda, Maryland
>> 20892, USA
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Pietro De Rossi, MD
>> --**---
>> Sapienza Università di Roma, Facoltà di Medicina e
>> Psicologia, Dipartimento
>> NESMOS (Neuroscienze, Salute Mentale, Organi di
>> Senso), Ospedale
>> Sant'Andrea, Via di Grottarossa 1035-1039, 00189
>> Roma
>>
>> NESMOS Department (Neurosciences, Mental Health and
>> Sensory Functions),
>> School of Medicine and Psychology, Sapienza
>> University, Sant?Andrea Hospital,
>> Via di Grottarossa 1035-1039,

Re: [Freesurfer] Cerebellar volume correction

[Louis Nicholas Vinke]

Hi Rachel,
Here are instructions for editing the aseg in tkmedit, it can also be done 
using Freeview.  Be sure to run mri_segstats again when you're done 
editing.


https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations#Editing

Alternatively, if the errors involve dura around the cerebellum being 
labeled as cerebellum you can edit the brainmask to remove the dura and 
then regenerate the aseg.mgz and stats.

-Louis

On Thu, 27 Sep 2012, Rachel Steinhorn wrote:


We'd like to obtain total cerebellar volumes.  There are errors within the
cerebellar segmentation as revealed in the aseg.mgz file.  Is there a method to
manually edit the cerebellar segmentation?

Thank You,
Rachel Steinhorn
___
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] long_mris_slopes command: temporal average calculation

[Shannon Kogachi]

Hi Martin,
 Each subject has 3-6 timepoints. They are all about one year apart.
Here's an example of the discrepancy: one subject with  5 timepoints had
volumes that ranged from 2.2-2.4. However, from the long_mris_slopes
command, the temporal average volume was calculated to be 1.67. Thanks for
your help!

-Shannon K.

On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter
wrote:

> Hi Shannon,
>
> long_mris_slopes works for surface maps (both thickness and volume
> should work). In both cases it should compute the temporal average.
>
> I have another scripts that works for stats files (long_stats_slopes) in
> the same way.
>
> How many time points do you have, how far apart (equally spaced?).
>
> Best, Martin
>
> On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote:
> > Hi Martin,
> >When I used the long_mris_slopes  command for the thickness, the
> > average thickness calculated in FreeSurfer was pretty similar to
> > averaging the values in FreeSurfer. Does this command only work
> > thickness measures and not for volume or area? Thanks!
> >
> > -Shannon
> >
> > On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter
> >  wrote:
> > Hi Shannon
> >
> > You probably mean average thickness.
> > My scripts compute the temporal average from the linear fit
> > (at mid time), which can be differed from simply averaging
> > values.
> > Best Martin
> >
> > Shannon Kogachi  wrote:
> > Hi,
> >  I had a question about how the temporal average is
> > calculated for subjects with multiple timepoints. I
> > used the long_mris_slopes command on a longitudinal
> > set of data. However, when I compared the average
> > volumes calculated through this command to the average
> > volumes calculated in excel after extracting the same
> > vertices at the individual timepoints, these values
> > did not match up. The average volumes calculated
> > through long_mris_slopes were smaller. Please let me
> > know if there is a way to explain this discrepancy.
> > Thank you!
> >
> > -Shannon K.
> >
> >
> >
> > __
> >
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Sent from my phone, please excuse brevity.
> > 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] CT Method Comparison

[Garikoitz Lerma-Usabiaga]

Hi,
You are right, this was one of the methods. The second one is as follows (I
copy the repeated steps):

For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on
colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if
it is out.


You have a registration between roi.nii and orig.mgz


You run mri_vol2surf on roi.nii to get lh.roi.mgh


I run mris_preproc for every subject to Colin27: mris_preproc --out
/subject/surf/ROI_toColin27.mgh --target Colin27 --hemi lh --meas thickness
--s subject

mri_segstats --seg /Colin27/surf/lh.roi.mgh --in
/subject/surf/ROI_to_Colin127.mgh --sum subject/stats/target_lh.ROI.stats


Thanks for your help,
Gari


Note:
You said: You run mri_cor2label (with --surf option) to convert lh.roi.mgh
into lh.roi.label
Just in case, this is how I run it:

   - mri_cor2label --i /subjects/Colin27/lh.ROI.mgh --surf Colin27 lh --id
   1 --l /subjects/Colin27/lh.ROI.label
   - mri_label2label --srclabel /subjects/Colin27/lh.ROI.label --srcsubject
   Colin27 --trgsubject subject --trglabel lh.ROI_Colin27_to_bert --regmethod
   surface --hemi lh




On 26/09/2012, at 23:56, Douglas N Greve  wrote:

Sorry, I'm still a little lost. Let me see if I have it right:


For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on
colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if
it is out.


You have a registration between roi.nii and orig.mgz


You run mri_vol2surf on roi.nii to get lh.roi.mgh


You run mri_cor2label (with --surf option) to convert lh.roi.mgh into
lh.roi.label


You run mri_label2label on lh.roi.label to map it into an individual subject


You run mris_anatomical_stats on the individual lh.roi.label file


Does this describe one of your processing streams correctly? If so, what is
the other processing stream (given in this kind of detail)?


doug




On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote:

I have both. In origin, the ROI-s are 2mm volume based .nii that I convert
to FS .mgh with  register.dat I obtained with bbregister.

-- In the case of label2label method I create the surface version with
mri_vol2surf (and the correspondence is perfect), and then use
mri_label2label in order to get the CT averages.

-- In the case of surf2surf, I use the volume based .mgh with mri_preproc
(mri_surf2surf)


thanks!

Gari


On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu >> wrote:


  So you have ROIs in Colin27 space and you want to map them into

  your CT space and compute average CT intensities over them? Are

  the ROIs volume-based or surface-based?

  doug



  On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote:


  Hi Doug,

  many thanks for your answer, I try to detail it more:


  1.- bbregister is registering two Colin27 brains. First one is

  a 2mm found in spm/canonical/single_subject_T1.nii, and second

  one is the FS_spm_Canonical found in SurfRend distribution. It

  was in .COR format and I run recon-all to have a modern

  version of it. As they are almost the same brain the

  registration matrix is quite simple and the registration was

  perfect. This way I had exactly the same ROI-s for Colin27 in

  SPM and in FS (it did not work that well for fsaverage, that's

  why I took this approach).


  2.- In any case, I have several ROI-s in Colin27 space in FS,

  and then when I try to obtain average CT values from my

  subjects I use these 2 different approaches: label2label and

  surf2surf.

  mri_anatomical_stats is run on the labels created by

  mri_label2label.



  If you think it will be of help I can send the detailed

  command line calls,

  thanks!

  Gari












  On Sat, Sep 22, 2012 at 12:47 AM, Douglas N Greve

  mailto:gr...@nmr.mgh.harvard.edu
>

  >>
wrote:


  Hi Gari, I'll need more information. I can't tell what you

  are doing.

  Eg, what is being registered with BBR? what is

  mris_anatomical_stats run

  on? Where does Colin27 come into it and why?

  doug


  On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga (Gari) wrote:

Dear Freesurfers,

We've been comparing 2 different methods to obtain CT averages

  for 4 Volume ROI-s (volume ROI-s were in Colin27 space).

We've used the 40 buckner subjects for the comparisons.


METHOD L2L:bbregister>>  mri_vol2surf (mgh)>>

   mri_binarize (mgh)>>  mri_cor2label (label)>>

   mri_label2label>>

   mris_anatomical_stats

METHOD S2S:   bbregister>>  mri_vol2surf>>  mri_preproc

  (mri_surf2surf)>>  mri_segstats



After performing t-test-s over the results, we can observe that

  the results are in many cases different.


-- Is there a way to choose the "best" method? Which one should

   

Re: [Freesurfer] CT Method Comparison

[Douglas Greve]

OK, got it (finally). I would not expect the answers to be identical, 
but I would expect them to be "close".  How close are they? If the ROI 
is very small, there might be appreciable differences between the two.


doug


On 9/27/12 6:26 PM, Garikoitz Lerma-Usabiaga wrote:

Hi,
You are right, this was one of the methods. The second one is as 
follows (I copy the repeated steps):


For a given ROI, you have a nifti file (roi.nii) in 2mm space defined 
on colin27. This ROI volume has a voxel value == 1 if it is in the 
ROI or 0 if it is out.


You have a registration between roi.nii and orig.mgz

You run mri_vol2surf on roi.nii to get lh.roi.mgh


I run mris_preproc for every subject to Colin27: mris_preproc --out 
/subject/surf/ROI_toColin27.mgh --target Colin27 --hemi lh --meas 
thickness --s subject


mri_segstats --seg /Colin27/surf/lh.roi.mgh --in 
/subject/surf/ROI_to_Colin127.mgh --sum subject/stats/target_lh.ROI.stats



Thanks for your help,
Gari


Note:
You said: You run mri_cor2label (with --surf option) to convert 
lh.roi.mgh into lh.roi.label

Just in case, this is how I run it:

  * mri_cor2label --i /subjects/Colin27/lh.ROI.mgh --surf Colin27 lh
--id 1 --l /subjects/Colin27/lh.ROI.label
  * mri_label2label --srclabel
/subjects/Colin27/lh.ROI.label --srcsubject Colin27 --trgsubject
subject --trglabel lh.ROI_Colin27_to_bert --regmethod surface
--hemi lh




On 26/09/2012, at 23:56, Douglas N Greve > wrote:



Sorry, I'm still a little lost. Let me see if I have it right:

For a given ROI, you have a nifti file (roi.nii) in 2mm space defined 
on colin27. This ROI volume has a voxel value == 1 if it is in the 
ROI or 0 if it is out.


You have a registration between roi.nii and orig.mgz

You run mri_vol2surf on roi.nii to get lh.roi.mgh

You run mri_cor2label (with --surf option) to convert lh.roi.mgh into 
lh.roi.label


You run mri_label2label on lh.roi.label to map it into an individual 
subject


You run mris_anatomical_stats on the individual lh.roi.label file

Does this describe one of your processing streams correctly? If so, 
what is the other processing stream (given in this kind of detail)?


doug



On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote:
I have both. In origin, the ROI-s are 2mm volume based .nii that I 
convert to FS .mgh with  register.dat I obtained with bbregister.
-- In the case of label2label method I create the surface version 
with mri_vol2surf (and the correspondence is perfect), and then use 
mri_label2label in order to get the CT averages.
-- In the case of surf2surf, I use the volume based .mgh with 
mri_preproc (mri_surf2surf)


thanks!
Gari

On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu> 
> wrote:


  So you have ROIs in Colin27 space and you want to map them into
  your CT space and compute average CT intensities over them? Are
  the ROIs volume-based or surface-based?
  doug


  On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote:

  Hi Doug,
  many thanks for your answer, I try to detail it more:

  1.- bbregister is registering two Colin27 brains. First one is
  a 2mm found in spm/canonical/single_subject_T1.nii, and second
  one is the FS_spm_Canonical found in SurfRend distribution. It
  was in .COR format and I run recon-all to have a modern
  version of it. As they are almost the same brain the
  registration matrix is quite simple and the registration was
  perfect. This way I had exactly the same ROI-s for Colin27 in
  SPM and in FS (it did not work that well for fsaverage, that's
  why I took this approach).

  2.- In any case, I have several ROI-s in Colin27 space in FS,
  and then when I try to obtain average CT values from my
  subjects I use these 2 different approaches: label2label and
  surf2surf.
  mri_anatomical_stats is run on the labels created by
  mri_label2label.


  If you think it will be of help I can send the detailed
  command line calls,
  thanks!
  Gari











  On Sat, Sep 22, 2012 at 12:47 AM, Douglas N Greve
  mailto:gr...@nmr.mgh.harvard.edu> 


  >> wrote:

  Hi Gari, I'll need more information. I can't tell what you
  are doing.
  Eg, what is being registered with BBR? what is
  mris_anatomical_stats run
  on? Where does Colin27 come into it and why?
  doug

  On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga (Gari) wrote:

Dear Freesurfers,
We've been comparing 2 different methods to obtain CT averages

  for 4 Volume ROI-s (volume ROI-s were in Colin27 space).

We've used the 40 buckner subjects for the comparisons.

METHOD L2L:bbregister>>  mri_vol2surf (mgh)>>

   mri_binarize (mgh)>>  mri_cor2label (label)>>