Re: [Freesurfer] Freesurfer dev error

[Bruce Fischl]

yes, that is fixed now
Bruce
On Sat, 2 Apr 2016, Nathan Malitz wrote:


recently download and trying the dev version of freesurfer 6.
it exited with this error


#@# Cortical Parc 2 lh Fri Apr  1 13:41:04 AEDT 2016
/usr/local/freesurfer6/subjects/test/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 testphp lh ../surf/lh.sphere.reg
/usr/local/freesurfer6/average/lh.CDatlas.2016-03-20
../label/lh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $
GCSAread(/usr/local/freesurfer6/average/lh.CDatlas.2016-03-20): could not
open file
reading atlas from /usr/local/freesurfer6/average/lh.CDatlas.2016-03-20...
No such file or directory
mris_ca_label: could not read classifier from
/usr/local/freesurfer6/average/lh.CDatlas.2016-03-20
No such file or directory


recon-all -s test exited with ERRORS at Fri Apr  1 13:41:08 AEDT 2016


This file doesn't exist in the directory, neither does the rh one, is it
called something else or missing from the build?

I'd prefer not to download 9GB again, is it available by itself?

any ideas?

--

Nathan Malitz


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[Freesurfer] Freesurfer dev error

[Nathan Malitz]

recently download and trying the dev version of freesurfer 6.
it exited with this error


#@# Cortical Parc 2 lh Fri Apr  1 13:41:04 AEDT 2016
/usr/local/freesurfer6/subjects/test/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz
-seed 1234 testphp lh ../surf/lh.sphere.reg /usr/local/freesurfer6/average
*/lh.CDatlas.2016-03-20* ../label/lh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $
GCSAread(/usr/local/freesurfer6/average/lh.CDatlas.2016-03-20): could not
open file
reading atlas from /usr/local/freesurfer6/average/lh.CDatlas.2016-03-20...
No such file or directory
mris_ca_label: could not read classifier from
/usr/local/freesurfer6/average/lh.CDatlas.2016-03-20
No such file or directory


recon-all -s test exited with ERRORS at Fri Apr  1 13:41:08 AEDT 2016


This file doesn't exist in the directory, neither does the rh one, is it
called something else or missing from the build?

I'd prefer not to download 9GB again, is it available by itself?

any ideas?

-- 

*Nathan Malitz*

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Re: [Freesurfer] How to view entire brain results in Freeview for LME data

[Jennifer Legault]

Hi Doug,

Thanks for your quick response!  When running the LME mass univariate
analysis, I am assuming this also includes subcortical structures,
correct?  From my understanding, subcortical areas are segmented as opposed
to parcellated.  The main thing I want to examine all the regions of the
brain that might change over time (as a function of the training task I've
given my participants), so I would look at both the aparc and the aseg
data, right?   Apologies if I've misunderstood your question.  For the aseg
data, I am currently having trouble with figuring out how to cluster
threshold the data (do i use mri_surfcluster with an argument to call the
aseg annotation or do I use mri_volcluster?) I would then want to visualize
the cluster thresholded data for subcortical structures in freeview.
Optimally, I would like to find some way to look at the whole brain in
Freeview to see these regions that have changed as a function of my
training task.

Best,

Jen

On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve 
wrote:

> You can put surface data back into the volume with mri_surf2vol (which
> will also merge left and right into one volume). What do you do with the
> aseg data?
>
> On 04/01/2016 10:46 AM, Jennifer Legault wrote:
> > Dear Freesurfer Experts,
> >
> > I have run my participants' longitudinal sMRI data through the
> > preprocessing longitudinal pipeline, ran the LME multivariate
> > analysis, cluster-thresholded the data, and am now trying to visualize
> > those results in Freeview (for some reason tksurfer is very, very slow
> > to run on my computer).  I am interested in the Fs volume
> > (thickness*area) measure.
> >
> > I noticed in the FsFast Tutorial
> > <
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel
> >,
> > that all the corrected results were able to be merged into one file
> > using the vlrmerge command.  In the beginning of the tutorial, it
> > states that fMRI and structuraI group analyses run similarly. / I was
> > therefore wondering if I can use the vlrmerge command (or some similar
> > command) for my LME data, such that I can view the following
> > information all in one file: both hemispheres, aparc and aseg.
> > / Currently I can only view the aparc results for each of the
> > hemispheres separately (and I haven't found a way to visualize the
> > aseg data).
> >
> > Thank you for taking the time to read this email.
> >
> > Best,
> >
> > Jennifer Legault
> > Ph.D candidate, Neuroscience
> > Brain, Language, and Computation Lab
> > The Pennsylvania State University
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
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Re: [Freesurfer] Labeled Nifti atlases

[Douglas N Greve]

do you want it in the volume or the surface? In the volume, there should 
be a file called $FREESURFER_HOME/subjects/fsaverage/mri/aparc+aseg.mgz
you can convert that to nifti

On 04/01/2016 02:20 PM, Gregory Book wrote:
> Are there any labeled nifti atlases that correspond to the freesurfer 
> parcellation atlases output from recon-all?
> I'm basically interested in visualization of group results.
> -Greg
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] Mismatch in dimensions using mri_label2vol

[Afzal, Afsana]

That works perfectly, thank you! 

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, April 01, 2016 11:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mismatch in dimensions using mri_label2vol

Use mri_label2label specifying the source and target subjects to be the
same, a regmethod as surface, and select the --outmask option

On 04/01/2016 11:37 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> I'm trying to map a cortical label onto the surface (i.e. extract a nifti 
> file for a particular label). So instead of a label.label file, it's a 
> label.nii that I can load in as an overlay in, say, tksurfer. Is there a way 
> to do this using freesurfer commands?
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, March 28, 2016 11:16 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Mismatch in dimensions using mri_label2vol
>
> Sorry, what are you trying to do? mri_label2vol maps a label (ie, ROI,
> segmentataion, annotation) into a volume space. Do you just want to map
> the surface overlay (fmcpr.sm4.fsaverage.lh.b0dc.nii) into the volume
> space? If so, use mri_surf2vol. You can use the version below (using
> method1 from the help)
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>
>
> On 03/28/2016 10:13 AM, Afzal, Afsana wrote:
>> Hi, Just wanted to follow up on the issue below regarding the
>> dimension of the mri_label2vol output.
>>
>>
>> Hi,
>>
>> I'm using mri_label2vol with the parameters below but the output .nii
>> volume has the shape 163842x1x1 while the input volume is27307x1x6.
>> This dimension mismatch is causing issues in our gPPI pipeline.
>>
>> How can I generate a .nii output file with the27307x1x6 dimension?
>>
>> mri_label2vol
>>  --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from
>> preproc step)
>>  --label label_name.label
>>  --o label_name.nii
>>  --identity
>>
>> Thanks,
>>
>> Afsana
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
>> [aaf...@mgh.harvard.edu]
>> *Sent:* Wednesday, March 23, 2016 2:44 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] Mismatch in dimensions using mri_label2vol
>>
>> Hi,
>>
>> I'm using mri_label2vol with the parameters below but the output .nii
>> volume has the shape 163842x1x1 while the input volume is27307x1x6.
>> This dimension mismatch is causing issues in our gPPI pipeline.
>>
>> How can I generate a .nii output file with the27307x1x6 dimension?
>>
>> mri_label2vol
>>  --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from
>> preproc step)
>>  --label label_name.label
>>  --o label_name.nii
>>  --identity
>>
>> Thanks,
>>
>> Afsana
>>
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>>
>> ___
>> 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] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

Hi Emad - I believe that it's not finding your freesurfer recons. They 
should be under the $SUBJECTS_DIR and have the same names for time points 
and longitudinal template as what is under your tracula output directory 
(if the latter is different from SUBJECTS_DIR).


Best,
a.y

On Fri, 1 Apr 2016, Emad Ahmadi wrote:


Hi Anastasia,

I’ve attached the log files. The cases are:

1. Case #2; time points: 2a, 2b; base template: 2tem
2. Case #3; time points: 3a, 3b; base template: 3tem

Thank you again for your help,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu



On Apr 1, 2016, at 10:49 AM, Anastasia Yendiki  
wrote:


Hi Emad - The error happens at the very beginning, so I'm wondering if 
something went wrong in the previous steps, before -path. Can you please send 
me the entire trac-all.log of one of your subjects? Thank you!

a.y

On Wed, 30 Mar 2016, Emad Ahmadi wrote:


Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all -prep 
& -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu

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[Freesurfer] Labeled Nifti atlases

[Gregory Book]

Are there any labeled nifti atlases that correspond to the freesurfer
parcellation atlases output from recon-all?
I'm basically interested in visualization of group results.
-Greg
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Re: [Freesurfer] Longitudinal recon-all fail

[Martin Reuter]

Hi Sneha,

Yes, mixing versions could also produce problems. 5.1 works in native 
spaces all the way trough to the long runs, while 5.3 works in the base 
space for the long runs. Don't mix versions.


Best, Martin


On 04/01/2016 12:38 PM, Sneha Pandya wrote:


Hi Martin,


Yes, I indeed checked the log file and saw so many errors, and was 
therefore very surprised as to how did it run through the pipeline 
without any error message. Thank you so much. I shall look at the 
specs for the disk space and notify if something unusual occurs. But 
its strange that we ran few more after similar failures and they seem 
to have run fine without these issues.



Also I wanted to point out that we are running these cases from two 
different servers pointing to same mount directory where all the 
processing has been running. One version of FS is 5.1 as you notified 
and other is 5.3. It could have been possible that we ran 
cross-sectional and base from either of these servers and ran 
longitudinal from other. Could that also be part of the reason for its 
failure because of IO? Do you suggest we should stick to only one 
server for cross-section to longitudinal run for different time points 
of same subjects?



Thanks,

Sneha



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 


*Sent:* Friday, April 1, 2016 12:18 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Longitudinal recon-all fail
Hi Sneha,

looks like an IO problem, maybe the disk is full or the mount was broken?

Strange that is reports finished without error, when in fact there are 
many errors (if you scroll up you can see many 'file not found' 
messages). Anyway. This is 5.1 and very old. I would recommend to 
check the IO disk space thing above and rerun these cases.


Best, Martin


On 04/01/2016 11:36 AM, Sneha Pandya wrote:


Dear experts,


We are running longitudinal pipeline for bunch of our MS 
subjects. Longitudinal recon-all failed to create volumes and 
surfaces for few of our subjects. We ran cross-sectional and did all 
the edits on them and after that ran base script without any issues 
or errors. When we run longitudinal on them it runs recon-all fine 
without exiting with errors. However it did not create important 
surfaces and volumes. Please find attached log file for one of the 
longitudinal timepoints for details.



Not sure why did they fail only for few of them as we have ran 100s 
of them with no issue earlier. Any advice will be of great help!



Thanks,

Sneha




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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  :http://reuter.mit.edu  



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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Longitudinal recon-all fail

[Sneha Pandya]

Hi Martin,


Yes, I indeed checked the log file and saw so many errors, and was therefore 
very surprised as to how did it run through the pipeline without any error 
message. Thank you so much. I shall look at the specs for the disk space and 
notify if something unusual occurs. But its strange that we ran few more after 
similar failures and they seem to have run fine without these issues.


Also I wanted to point out that we are running these cases from two different 
servers pointing to same mount directory where all the processing has been 
running. One version of FS is 5.1 as you notified and other is 5.3. It could 
have been possible that we ran cross-sectional and base from either of these 
servers and ran longitudinal from other. Could that also be part of the reason 
for its failure because of IO? Do you suggest we should stick to only one 
server for cross-section to longitudinal run for different time points of same 
subjects?


Thanks,

Sneha


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: Friday, April 1, 2016 12:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal recon-all fail

Hi Sneha,

looks like an IO problem, maybe the disk is full or the mount was broken?

Strange that is reports finished without error, when in fact there are many 
errors (if you scroll up you can see many 'file not found' messages). Anyway. 
This is 5.1 and very old. I would recommend to check the IO disk space thing 
above and rerun these cases.

Best, Martin


On 04/01/2016 11:36 AM, Sneha Pandya wrote:

Dear experts,


We are running longitudinal pipeline for bunch of our MS subjects. Longitudinal 
recon-all failed to create volumes and surfaces for few of our subjects. We ran 
cross-sectional and did all the edits on them and after that ran base script 
without any issues or errors. When we run longitudinal on them it runs 
recon-all fine without exiting with errors. However it did not create important 
surfaces and volumes. Please find attached log file for one of the longitudinal 
timepoints for details.


Not sure why did they fail only for few of them as we have ran 100s of them 
with no issue earlier. Any advice will be of great help!


Thanks,

Sneha




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


--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : 
http://reuter.mit.edu
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Re: [Freesurfer] Longitudinal recon-all fail

[Martin Reuter]

Hi Sneha,

looks like an IO problem, maybe the disk is full or the mount was broken?

Strange that is reports finished without error, when in fact there are 
many errors (if you scroll up you can see many 'file not found' 
messages). Anyway. This is 5.1 and very old. I would recommend to check 
the IO disk space thing above and rerun these cases.


Best, Martin


On 04/01/2016 11:36 AM, Sneha Pandya wrote:


Dear experts,


We are running longitudinal pipeline for bunch of our MS 
subjects. Longitudinal recon-all failed to create volumes and surfaces 
for few of our subjects. We ran cross-sectional and did all the edits 
on them and after that ran base script without any issues or errors. 
When we run longitudinal on them it runs recon-all fine without 
exiting with errors. However it did not create important surfaces and 
volumes. Please find attached log file for one of the longitudinal 
timepoints for details.



Not sure why did they fail only for few of them as we have ran 100s of 
them with no issue earlier. Any advice will be of great help!



Thanks,

Sneha




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Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] I: FS-FAST bandpass filtering

[Douglas N Greve]

Not by default, look at mkanalysis-sess -help for more details, 
especially the -hpc and -lpc options.


Hi,
I'm wondering whether the FS-FAST performed bandpass filtering.

Stefano


On 04/01/2016 03:11 AM, std...@virgilio.it wrote:
>
>
>
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Re: [Freesurfer] Mismatch in dimensions using mri_label2vol

[Douglas N Greve]

Use mri_label2label specifying the source and target subjects to be the 
same, a regmethod as surface, and select the --outmask option

On 04/01/2016 11:37 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> I'm trying to map a cortical label onto the surface (i.e. extract a nifti 
> file for a particular label). So instead of a label.label file, it's a 
> label.nii that I can load in as an overlay in, say, tksurfer. Is there a way 
> to do this using freesurfer commands?
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, March 28, 2016 11:16 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Mismatch in dimensions using mri_label2vol
>
> Sorry, what are you trying to do? mri_label2vol maps a label (ie, ROI,
> segmentataion, annotation) into a volume space. Do you just want to map
> the surface overlay (fmcpr.sm4.fsaverage.lh.b0dc.nii) into the volume
> space? If so, use mri_surf2vol. You can use the version below (using
> method1 from the help)
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
>
>
> On 03/28/2016 10:13 AM, Afzal, Afsana wrote:
>> Hi, Just wanted to follow up on the issue below regarding the
>> dimension of the mri_label2vol output.
>>
>>
>> Hi,
>>
>> I'm using mri_label2vol with the parameters below but the output .nii
>> volume has the shape 163842x1x1 while the input volume is27307x1x6.
>> This dimension mismatch is causing issues in our gPPI pipeline.
>>
>> How can I generate a .nii output file with the27307x1x6 dimension?
>>
>> mri_label2vol
>>  --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from
>> preproc step)
>>  --label label_name.label
>>  --o label_name.nii
>>  --identity
>>
>> Thanks,
>>
>> Afsana
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>> 
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
>> [aaf...@mgh.harvard.edu]
>> *Sent:* Wednesday, March 23, 2016 2:44 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] Mismatch in dimensions using mri_label2vol
>>
>> Hi,
>>
>> I'm using mri_label2vol with the parameters below but the output .nii
>> volume has the shape 163842x1x1 while the input volume is27307x1x6.
>> This dimension mismatch is causing issues in our gPPI pipeline.
>>
>> How can I generate a .nii output file with the27307x1x6 dimension?
>>
>> mri_label2vol
>>  --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from
>> preproc step)
>>  --label label_name.label
>>  --o label_name.nii
>>  --identity
>>
>> Thanks,
>>
>> Afsana
>>
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] How to view entire brain results in Freeview for LME data

[Douglas N Greve]

You can put surface data back into the volume with mri_surf2vol (which 
will also merge left and right into one volume). What do you do with the 
aseg data?

On 04/01/2016 10:46 AM, Jennifer Legault wrote:
> Dear Freesurfer Experts,
>
> I have run my participants' longitudinal sMRI data through the 
> preprocessing longitudinal pipeline, ran the LME multivariate 
> analysis, cluster-thresholded the data, and am now trying to visualize 
> those results in Freeview (for some reason tksurfer is very, very slow 
> to run on my computer).  I am interested in the Fs volume 
> (thickness*area) measure.
>
> I noticed in the FsFast Tutorial 
> ,
>  
> that all the corrected results were able to be merged into one file 
> using the vlrmerge command.  In the beginning of the tutorial, it 
> states that fMRI and structuraI group analyses run similarly. / I was 
> therefore wondering if I can use the vlrmerge command (or some similar 
> command) for my LME data, such that I can view the following 
> information all in one file: both hemispheres, aparc and aseg. 
> / Currently I can only view the aparc results for each of the 
> hemispheres separately (and I haven't found a way to visualize the 
> aseg data).
>
> Thank you for taking the time to read this email.
>
> Best,
>
> Jennifer Legault
> Ph.D candidate, Neuroscience
> Brain, Language, and Computation Lab
> The Pennsylvania State University
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] tksurfer scale bar

[Bruce Fischl]

is the spm data mapped to the surface (with mri_vol2surf) or a volume?
On 
Fri, 1 Apr 2016, Michael Asghar wrote:



Hi again

I think I've figured out how freeview works, but I'm having trouble loading 
functional data taken from SPM12, and overlaying it on a surface in freesurfer.
I can load the lh.inflated and also load the spmT.nii file, but I'm just 
getting a grey surface, and playing with the scale doesn't help.
I've also tried using mri_convert to get the nii into mgz, but still get the 
same results.

Sorry for being a pain!
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael Asghar
Sent: 01 April 2016 14:59
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar

Thanks

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 01 April 2016 14:58
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar


freeview -f lh.inflated:overlay=lh.pet_data.mgz

would be a good place to start. There's lots of stuff on the wiki cheers Bruce



On Fri, 1 Apr 2016, Michael
Asghar wrote:


Oh, I didn’t know that. I've been advised to use tksurfer (we're trying to get 
nice images of PET data overlaid on surfaces).

I haven't got a clue how to use freeview - any simple commands to load up a 
surface, overlay some statistical data?

Thanks!
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: 01 April 2016 14:44
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar

Hi Michael

tksurfer is deprecated - have you tried this in freeview?

cheers
Bruce
On Fri, 1 Apr
2016, Michael Asghar wrote:



Hi Freesurfer

 

I’m struggling with trying to edit the scale bar in tksurfer.
Commands like ‘set scalebar_bright 240’ work, but draw_scalebar gives
an invalid command error.

I’ve tried redrawing, but it doesn’t help.

 

Basically, I want the black background to become white (can do it via
convert –fill white –opaque black input.tiff output.tiff), but the
numbers on the scalebar are invisible now – I need the scale bar text to be 
black.

 

Also, I get two bits to my scalebar, e.g. negative values at the
bottom from
-5 to -3, then a grey gap and then positive 3 to 5 in hot colours.
How do I get just the positive T values in a suitable distance (they
are currently squeezed up at either side).

 

Thanks!

Michael



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Re: [Freesurfer] tksurfer scale bar

[Douglas N Greve]

you can also try tksurferfv. this is a frontend for freeview that takes 
tksurfer-style arguments

On 04/01/2016 09:57 AM, Bruce Fischl wrote:
>
> freeview -f lh.inflated:overlay=lh.pet_data.mgz
>
> would be a good place to start. There's lots of stuff on the wiki
> cheers
> Bruce
>
>
>
> On Fri, 1 Apr 2016, Michael Asghar wrote:
>
>> Oh, I didn’t know that. I've been advised to use tksurfer (we're 
>> trying to get nice images of PET data overlaid on surfaces).
>>
>> I haven't got a clue how to use freeview - any simple commands to 
>> load up a surface, overlay some statistical data?
>>
>> Thanks!
>> Michael
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>> Fischl
>> Sent: 01 April 2016 14:44
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] tksurfer scale bar
>>
>> Hi Michael
>>
>> tksurfer is deprecated - have you tried this in freeview?
>>
>> cheers
>> Bruce
>> On Fri, 1 Apr
>> 2016, Michael Asghar wrote:
>>
>>>
>>> Hi Freesurfer
>>>
>>>
>>>
>>> I’m struggling with trying to edit the scale bar in tksurfer. Commands
>>> like ‘set scalebar_bright 240’ work, but draw_scalebar gives an
>>> invalid command error.
>>>
>>> I’ve tried redrawing, but it doesn’t help.
>>>
>>>
>>>
>>> Basically, I want the black background to become white (can do it via
>>> convert –fill white –opaque black input.tiff output.tiff), but the
>>> numbers on the scalebar are invisible now – I need the scale bar 
>>> text to be black.
>>>
>>>
>>>
>>> Also, I get two bits to my scalebar, e.g. negative values at the
>>> bottom from
>>> -5 to -3, then a grey gap and then positive 3 to 5 in hot colours. How
>>> do I get just the positive T values in a suitable distance (they are
>>> currently squeezed up at either side).
>>>
>>>
>>>
>>> Thanks!
>>>
>>> Michael
>>>
>>>
>>>
>>> This message and any attachment are intended solely for the addressee
>>> and may contain confidential information. If you have received this
>>> message in error, please send it back to me, and immediately delete it.
>>>
>>> Please do not use, copy or disclose the information contained in this
>>> message or in any attachment.  Any views or opinions expressed by the
>>> author of this email do not necessarily reflect the views of the
>>> University of Nottingham.
>>>
>>> This message has been checked for viruses but the contents of an
>>> attachment may still contain software viruses which could damage your
>>> computer system, you are advised to perform your own checks. Email
>>> communications with the University of Nottingham may be monitored as
>>> permitted by UK legislation.
>>>
>>>
>>
>>
>>
>>
>> This message and any attachment are intended solely for the addressee
>> and may contain confidential information. If you have received this
>> message in error, please send it back to me, and immediately delete it.
>>
>> Please do not use, copy or disclose the information contained in this
>> message or in any attachment.  Any views or opinions expressed by the
>> author of this email do not necessarily reflect the views of the
>> University of Nottingham.
>>
>> This message has been checked for viruses but the contents of an
>> attachment may still contain software viruses which could damage your
>> computer system, you are advised to perform your own checks. Email
>> communications with the University of Nottingham may be monitored as
>> permitted by UK legislation.
>>
>>
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>>
>>
>>
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

Hi Emad - The error happens at the very beginning, so I'm wondering if 
something went wrong in the previous steps, before -path. Can you please 
send me the entire trac-all.log of one of your subjects? Thank you!


a.y

On Wed, 30 Mar 2016, Emad Ahmadi wrote:


Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all -prep 
& -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu
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[Freesurfer] How to view entire brain results in Freeview for LME data

[Jennifer Legault]

Dear Freesurfer Experts,

I have run my participants' longitudinal sMRI data through the
preprocessing longitudinal pipeline, ran the LME multivariate analysis,
cluster-thresholded the data, and am now trying to visualize those results
in Freeview (for some reason tksurfer is very, very slow to run on my
computer).  I am interested in the Fs volume (thickness*area) measure.

I noticed in the FsFast Tutorial
,
that all the corrected results were able to be merged into one file using
the vlrmerge command.  In the beginning of the tutorial, it states that
fMRI and structuraI group analyses run similarly. * I was therefore
wondering if I can use the vlrmerge command (or some similar command) for
my LME data, such that I can view the following information all in one
file: both hemispheres, aparc and aseg. * Currently I can only view the
aparc results for each of the hemispheres separately (and I haven't found a
way to visualize the aseg data).

Thank you for taking the time to read this email.

Best,

Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
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Re: [Freesurfer] tksurfer scale bar

[Michael Asghar]

Hi again

I think I've figured out how freeview works, but I'm having trouble loading 
functional data taken from SPM12, and overlaying it on a surface in freesurfer.
I can load the lh.inflated and also load the spmT.nii file, but I'm just 
getting a grey surface, and playing with the scale doesn't help.
I've also tried using mri_convert to get the nii into mgz, but still get the 
same results.

Sorry for being a pain!
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael Asghar
Sent: 01 April 2016 14:59
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar

Thanks

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 01 April 2016 14:58
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar


freeview -f lh.inflated:overlay=lh.pet_data.mgz

would be a good place to start. There's lots of stuff on the wiki cheers Bruce



On Fri, 1 Apr 2016, Michael
Asghar wrote:

> Oh, I didn’t know that. I've been advised to use tksurfer (we're trying to 
> get nice images of PET data overlaid on surfaces).
>
> I haven't got a clue how to use freeview - any simple commands to load up a 
> surface, overlay some statistical data?
>
> Thanks!
> Michael
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: 01 April 2016 14:44
> To: Freesurfer support list
> Subject: Re: [Freesurfer] tksurfer scale bar
>
> Hi Michael
>
> tksurfer is deprecated - have you tried this in freeview?
>
> cheers
> Bruce
> On Fri, 1 Apr
> 2016, Michael Asghar wrote:
>
>>
>> Hi Freesurfer
>>
>>  
>>
>> I’m struggling with trying to edit the scale bar in tksurfer. 
>> Commands like ‘set scalebar_bright 240’ work, but draw_scalebar gives 
>> an invalid command error.
>>
>> I’ve tried redrawing, but it doesn’t help.
>>
>>  
>>
>> Basically, I want the black background to become white (can do it via 
>> convert –fill white –opaque black input.tiff output.tiff), but the 
>> numbers on the scalebar are invisible now – I need the scale bar text to be 
>> black.
>>
>>  
>>
>> Also, I get two bits to my scalebar, e.g. negative values at the 
>> bottom from
>> -5 to -3, then a grey gap and then positive 3 to 5 in hot colours. 
>> How do I get just the positive T values in a suitable distance (they 
>> are currently squeezed up at either side).
>>
>>  
>>
>> Thanks!
>>
>> Michael
>>
>>
>>
>> This message and any attachment are intended solely for the addressee 
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>> University of Nottingham.
>>
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>> attachment may still contain software viruses which could damage your 
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>> permitted by UK legislation.
>>
>>
>
>
>
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Re: [Freesurfer] tksurfer scale bar

[Michael Asghar]

Thanks

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 01 April 2016 14:58
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar


freeview -f lh.inflated:overlay=lh.pet_data.mgz

would be a good place to start. There's lots of stuff on the wiki cheers Bruce



On Fri, 1 Apr 2016, Michael
Asghar wrote:

> Oh, I didn’t know that. I've been advised to use tksurfer (we're trying to 
> get nice images of PET data overlaid on surfaces).
>
> I haven't got a clue how to use freeview - any simple commands to load up a 
> surface, overlay some statistical data?
>
> Thanks!
> Michael
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: 01 April 2016 14:44
> To: Freesurfer support list
> Subject: Re: [Freesurfer] tksurfer scale bar
>
> Hi Michael
>
> tksurfer is deprecated - have you tried this in freeview?
>
> cheers
> Bruce
> On Fri, 1 Apr
> 2016, Michael Asghar wrote:
>
>>
>> Hi Freesurfer
>>
>>  
>>
>> I’m struggling with trying to edit the scale bar in tksurfer. 
>> Commands like ‘set scalebar_bright 240’ work, but draw_scalebar gives 
>> an invalid command error.
>>
>> I’ve tried redrawing, but it doesn’t help.
>>
>>  
>>
>> Basically, I want the black background to become white (can do it via 
>> convert –fill white –opaque black input.tiff output.tiff), but the 
>> numbers on the scalebar are invisible now – I need the scale bar text to be 
>> black.
>>
>>  
>>
>> Also, I get two bits to my scalebar, e.g. negative values at the 
>> bottom from
>> -5 to -3, then a grey gap and then positive 3 to 5 in hot colours. 
>> How do I get just the positive T values in a suitable distance (they 
>> are currently squeezed up at either side).
>>
>>  
>>
>> Thanks!
>>
>> Michael
>>
>>
>>
>> This message and any attachment are intended solely for the addressee 
>> and may contain confidential information. If you have received this 
>> message in error, please send it back to me, and immediately delete it.
>>
>> Please do not use, copy or disclose the information contained in this 
>> message or in any attachment.  Any views or opinions expressed by the 
>> author of this email do not necessarily reflect the views of the 
>> University of Nottingham.
>>
>> This message has been checked for viruses but the contents of an 
>> attachment may still contain software viruses which could damage your 
>> computer system, you are advised to perform your own checks. Email 
>> communications with the University of Nottingham may be monitored as 
>> permitted by UK legislation.
>>
>>
>
>
>
>
> This message and any attachment are intended solely for the addressee 
> and may contain confidential information. If you have received this 
> message in error, please send it back to me, and immediately delete it.
>
> Please do not use, copy or disclose the information contained in this 
> message or in any attachment.  Any views or opinions expressed by the 
> author of this email do not necessarily reflect the views of the 
> University of Nottingham.
>
> This message has been checked for viruses but the contents of an 
> attachment may still contain software viruses which could damage your 
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> permitted by UK legislation.
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>
> ___
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>
>
>




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Re: [Freesurfer] tksurfer scale bar

[Bruce Fischl]

freeview -f lh.inflated:overlay=lh.pet_data.mgz

would be a good place to start. There's lots of stuff on the wiki
cheers
Bruce



On Fri, 1 Apr 2016, Michael 
Asghar wrote:



Oh, I didn’t know that. I've been advised to use tksurfer (we're trying to get 
nice images of PET data overlaid on surfaces).

I haven't got a clue how to use freeview - any simple commands to load up a 
surface, overlay some statistical data?

Thanks!
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 01 April 2016 14:44
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar

Hi Michael

tksurfer is deprecated - have you tried this in freeview?

cheers
Bruce
On Fri, 1 Apr
2016, Michael Asghar wrote:



Hi Freesurfer

 

I’m struggling with trying to edit the scale bar in tksurfer. Commands
like ‘set scalebar_bright 240’ work, but draw_scalebar gives an
invalid command error.

I’ve tried redrawing, but it doesn’t help.

 

Basically, I want the black background to become white (can do it via
convert –fill white –opaque black input.tiff output.tiff), but the
numbers on the scalebar are invisible now – I need the scale bar text to be 
black.

 

Also, I get two bits to my scalebar, e.g. negative values at the
bottom from
-5 to -3, then a grey gap and then positive 3 to 5 in hot colours. How
do I get just the positive T values in a suitable distance (they are
currently squeezed up at either side).

 

Thanks!

Michael



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University of Nottingham.

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communications with the University of Nottingham may be monitored as
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University of Nottingham.

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Re: [Freesurfer] tksurfer scale bar

[Michael Asghar]

Oh, I didn’t know that. I've been advised to use tksurfer (we're trying to get 
nice images of PET data overlaid on surfaces).

I haven't got a clue how to use freeview - any simple commands to load up a 
surface, overlay some statistical data?

Thanks!
Michael

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 01 April 2016 14:44
To: Freesurfer support list
Subject: Re: [Freesurfer] tksurfer scale bar

Hi Michael

tksurfer is deprecated - have you tried this in freeview?

cheers
Bruce
On Fri, 1 Apr
2016, Michael Asghar wrote:

> 
> Hi Freesurfer
> 
>  
> 
> I’m struggling with trying to edit the scale bar in tksurfer. Commands 
> like ‘set scalebar_bright 240’ work, but draw_scalebar gives an 
> invalid command error.
> 
> I’ve tried redrawing, but it doesn’t help.
> 
>  
> 
> Basically, I want the black background to become white (can do it via 
> convert –fill white –opaque black input.tiff output.tiff), but the 
> numbers on the scalebar are invisible now – I need the scale bar text to be 
> black.
> 
>  
> 
> Also, I get two bits to my scalebar, e.g. negative values at the 
> bottom from
> -5 to -3, then a grey gap and then positive 3 to 5 in hot colours. How 
> do I get just the positive T values in a suitable distance (they are 
> currently squeezed up at either side).
> 
>  
> 
> Thanks!
> 
> Michael
> 
> 
> 
> This message and any attachment are intended solely for the addressee 
> and may contain confidential information. If you have received this 
> message in error, please send it back to me, and immediately delete it.
> 
> Please do not use, copy or disclose the information contained in this 
> message or in any attachment.  Any views or opinions expressed by the 
> author of this email do not necessarily reflect the views of the 
> University of Nottingham.
> 
> This message has been checked for viruses but the contents of an 
> attachment may still contain software viruses which could damage your 
> computer system, you are advised to perform your own checks. Email 
> communications with the University of Nottingham may be monitored as 
> permitted by UK legislation.
> 
>




This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it. 

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
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Re: [Freesurfer] tksurfer scale bar

[Bruce Fischl]

Hi Michael

tksurfer is deprecated - have you tried this in freeview?

cheers
Bruce
On Fri, 1 Apr 
2016, Michael Asghar wrote:




Hi Freesurfer

 

I’m struggling with trying to edit the scale bar in tksurfer. Commands like
‘set scalebar_bright 240’ work, but draw_scalebar gives an invalid command
error.

I’ve tried redrawing, but it doesn’t help.

 

Basically, I want the black background to become white (can do it via
convert –fill white –opaque black input.tiff output.tiff), but the numbers
on the scalebar are invisible now – I need the scale bar text to be black.

 

Also, I get two bits to my scalebar, e.g. negative values at the bottom from
-5 to -3, then a grey gap and then positive 3 to 5 in hot colours. How do I
get just the positive T values in a suitable distance (they are currently
squeezed up at either side).

 

Thanks!

Michael



This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it. 


Please do not use, copy or disclose the information contained in this
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author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
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[Freesurfer] tksurfer scale bar

[Michael Asghar]

Hi Freesurfer

I'm struggling with trying to edit the scale bar in tksurfer. Commands like 
'set scalebar_bright 240' work, but draw_scalebar gives an invalid command 
error.
I've tried redrawing, but it doesn't help.

Basically, I want the black background to become white (can do it via convert 
-fill white -opaque black input.tiff output.tiff), but the numbers on the 
scalebar are invisible now - I need the scale bar text to be black.

Also, I get two bits to my scalebar, e.g. negative values at the bottom from -5 
to -3, then a grey gap and then positive 3 to 5 in hot colours. How do I get 
just the positive T values in a suitable distance (they are currently squeezed 
up at either side).

Thanks!
Michael




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and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it. 

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
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Re: [Freesurfer] Improve normalization with own average subject

[Bruce Fischl]

Hi pfannmoe

that page looks pretty good to me. YOu need to create a new folding atlas 
which we typically store in .tif format using mris_make_template. This is 
usually done by picking one subject, registering all your subjects to that 
template (.tif file), recreating the template, reregistering and so on. 
Usually this converges after 2-3 rounds.

cheers
Bruce


On Fri, 1 Apr 2016, 
pfannmo...@uni-greifswald.de wrote:

> Dear Experts,
>
> I am currently working with the non-linear FreeSurfer normalization.
> We have a small group of subjects N = 12 and in each brain we
> identified a single position with a fMRI localizer. The task is a
> group comparison of the individual results for this position.
> Therefore, the coordinates of each position in FSaverage was
> determined using mri_label2label. The radius of the region is an
> important quantity in my investigations. A smaller radius would help
> me a lot in my data processing. I tried to decrease the radius by
> generating a new group space template from my 12 subjects with
> make_average_subject. Then I used mri_label2label to determine the
> coordinates in the new group space template. Unfortunately, there
> was no difference in the radius. The intention behind this procedure
> was to achieve an improved normalization of the subjects. I have read
> much about this topic in the mailing list, but there are many details
> in the processing which I am not yet aware of. So, my question is if
> I proceeded the best possible way or if there is a better alternative
> to improve the normalization. Would it help to generate a new template
> as outlined in the second part on this web tutorial (chapter: Creating
> a registration template from scratch):
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
>
> or do I need to use mris_register with my new template and my 12
> subjects instead of mri_label2label in order to benfit from my new
> template as generated by make_average_subject (also outlined in the
> web tutorial in the chapter: Creating a registration template
> initialized with FreeSurfer template)?
>
> Even a small decrease in the radius would help to improve my results.
>
> Thanks in advance
>
> pfannmoe
>
>
>
>
>
>
>
>
> ___
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>
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[Freesurfer] Improve normalization with own average subject

[pfannmoelj]

Dear Experts,

I am currently working with the non-linear FreeSurfer normalization. 
We have a small group of subjects N = 12 and in each brain we 
identified a single position with a fMRI localizer. The task is a 
group comparison of the individual results for this position. 
Therefore, the coordinates of each position in FSaverage was 
determined using mri_label2label. The radius of the region is an 
important quantity in my investigations. A smaller radius would help 
me a lot in my data processing. I tried to decrease the radius by 
generating a new group space template from my 12 subjects with 
make_average_subject. Then I used mri_label2label to determine the 
coordinates in the new group space template. Unfortunately, there 
was no difference in the radius. The intention behind this procedure 
was to achieve an improved normalization of the subjects. I have read 
much about this topic in the mailing list, but there are many details 
in the processing which I am not yet aware of. So, my question is if 
I proceeded the best possible way or if there is a better alternative 
to improve the normalization. Would it help to generate a new template 
as outlined in the second part on this web tutorial (chapter: Creating 
a registration template from scratch):

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

or do I need to use mris_register with my new template and my 12 
subjects instead of mri_label2label in order to benfit from my new 
template as generated by make_average_subject (also outlined in the 
web tutorial in the chapter: Creating a registration template 
initialized with FreeSurfer template)?

Even a small decrease in the radius would help to improve my results. 

Thanks in advance

pfannmoe

 






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[Freesurfer] I: FS-FAST bandpass filtering

[stdp82]

--- Begin Message ---
Hi,I'm wondering whether the FS-FAST performed bandpass filtering.
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