date:20170126

Re: [Freesurfer] White matter probability map.

2017-01-26 Thread miracle ozzoude

hello doug,
Thank you.
1) where can i find this lta file? I looked for it in the mri and surface
folders but it wasn't there. do i need to run another command in order to
generate it?
2) Is this the right command? mri_compute_volume_fractions --o pvf --reg
filename.lta (location of .lta)
3)Also, Is there a command that converts the results from
mri_compute_volume_fractions (which is the volume fraction map) into
probability map?
3) I searched the forum and various posts mentioned using mri_ca_label to
create probablity maps of tissue segmentations (e.g.,
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046425.html).
Is this truth? If yes, is it possible to use it with
mri_compute_volume_fractions or not?
Thank you,
Paul.

On Thu, Jan 26, 2017 at 6:24 PM, Douglas N Greve 
wrote:

> Run it something like
>
> mri_compute_volume_fractions --o pvf --reg register.dof6.lta
>
> where the lta file is a registration file between the FS anat and the
> volume that you want to get the PVFs for. The output will have a base
> name of pvf, eg,
>
> pvf.cortex.mgz  pvf.csf.mgz  pvf.subcort_gm.mgz  pvf.wm.mgz
>
>
>
>
>
> On 01/26/2017 06:14 PM, miracoo...@gmail.com wrote:
> > Hello Douglas,
> > Thank you. When I looked up the command with --help, it said " computes
> partial volume fractions for cortex, subcortical GM, WM and CSf". What
> volume do I give the command as an input? T1, orig.mgz ‎.
> > Best,
> > Miracle
> >
> > Sent from my BlackBerry 10 smartphone.
> >Original Message
> > From: Douglas N Greve‎
> > Sent: Thursday, January 26, 2017 5:54 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Reply To: Freesurfer support list
> > Subject: Re: [Freesurfer] White matter probability map.
> >
> > ps, it is not a probability map per se but the volume fraction (0-1) map
> >
> >
> > On 01/26/2017 05:52 PM, Douglas N Greve wrote:
> >> Try mri_compute_volume_fractions
> >>
> >>
> >> On 01/26/2017 05:49 PM, miracoo...@gmail.com wrote:
> >>> Hello Freesurfer,
> >>> Is there a way to extract tissue probability map for white matter
> >>> in FS. Thank you
> >>> Best,
> >>> Miracle
> >>> Sent from my BlackBerry 10 smartphone.
> >>>
> >>>
> >>>
> >>> ___
> >>> 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
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>
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Re: [Freesurfer] mri_label2label problem

2017-01-26 Thread Bronwyn Overs

Hi Doug,

Yes i was visualising it on fsaverage. I switched to sub003 and the ROI looks 
perfect. What a simple mistake, thanks for your help.
Kind regards,
Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au  
  
 

> On 27 Jan 2017, at 10:26 am, Douglas N Greve  
> wrote:
> 
> Are you visualizing the output on subject sub003? It looks like fsaverage
> 
> 
> On 01/26/2017 06:23 PM, Bronwyn Overs wrote:
>> Hi Mailing list,
>> 
>> I have been running the mri_label2label command and have encountered a 
>> problem with the newly generated label. The command I am running is as 
>> follows:
>> 
>> mri_label2label --srclabel 
>> "$SUBJECTS_DIR/fsaverage/label/lh.sm20.lme.test.B2-0001.label" 
>> --srcsubject fsaverage_mod --trglabel "Test.label" --trgsubject 
>> “sub003" --regmethod surface --hemi lh
>> 
>> When I visualise the original label there is a distinct temporal ROI 
>> outlined. However, when I load the label for my individual 
>> subject there is no temporal ROI outlined, instead I see numerous 
>> widely dispersed vertices highlighted across the whole surface of the 
>> cortex. Can you identify what the issue is? I have attached images 
>> that show the input and output labels overlayed on an inflated surface.
>> 
>> 
>> 
>> 
>> 
>> Kind regards,
>> 
>> Bronwyn Overs
>> Research Assistant
>> 
>> Neuroscience Research Australia
>> 
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>> 
>> neura.edu.au  > >
>> 
>> Follow @neuraustralia on twitter 
>> > >Follow NeuRA on facebook 
>> > >Subscribe to 
>> the NeuRA Magazine > >
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> 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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> 
> 
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Re: [Freesurfer] mri_label2label problem

2017-01-26 Thread Douglas N Greve

Are you visualizing the output on subject sub003? It looks like fsaverage


On 01/26/2017 06:23 PM, Bronwyn Overs wrote:
> Hi Mailing list,
>
> I have been running the mri_label2label command and have encountered a 
> problem with the newly generated label. The command I am running is as 
> follows:
>
> mri_label2label --srclabel 
> "$SUBJECTS_DIR/fsaverage/label/lh.sm20.lme.test.B2-0001.label" 
> --srcsubject fsaverage_mod --trglabel "Test.label" --trgsubject 
> “sub003" --regmethod surface --hemi lh
>
> When I visualise the original label there is a distinct temporal ROI 
> outlined. However, when I load the label for my individual 
> subject there is no temporal ROI outlined, instead I see numerous 
> widely dispersed vertices highlighted across the whole surface of the 
> cortex. Can you identify what the issue is? I have attached images 
> that show the input and output labels overlayed on an inflated surface.
>
>
>
>
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au 
>
> Follow @neuraustralia on twitter 
> Follow NeuRA on facebook 
> Subscribe to 
> the NeuRA Magazine 
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 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] White matter probability map.

2017-01-26 Thread Douglas N Greve

Run it something like

mri_compute_volume_fractions --o pvf --reg register.dof6.lta

where the lta file is a registration file between the FS anat and the 
volume that you want to get the PVFs for. The output will have a base 
name of pvf, eg,

pvf.cortex.mgz  pvf.csf.mgz  pvf.subcort_gm.mgz  pvf.wm.mgz





On 01/26/2017 06:14 PM, miracoo...@gmail.com wrote:
> Hello Douglas,
> Thank you. When I looked up the command with --help, it said " computes 
> partial volume fractions for cortex, subcortical GM, WM and CSf". What volume 
> do I give the command as an input? T1, orig.mgz ‎.
> Best,
> Miracle
>
> Sent from my BlackBerry 10 smartphone.
>Original Message
> From: Douglas N Greve‎
> Sent: Thursday, January 26, 2017 5:54 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] White matter probability map.
>
> ps, it is not a probability map per se but the volume fraction (0-1) map
>
>
> On 01/26/2017 05:52 PM, Douglas N Greve wrote:
>> Try mri_compute_volume_fractions
>>
>>
>> On 01/26/2017 05:49 PM, miracoo...@gmail.com wrote:
>>> Hello Freesurfer,
>>> Is there a way to extract tissue probability map for white matter
>>> in FS. Thank you
>>> Best,
>>> Miracle
>>> Sent from my BlackBerry 10 smartphone.
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] White matter probability map.

2017-01-26 Thread miracooloz

Hello Douglas, 
Thank you. When I looked up the command with --help, it said " computes partial 
volume fractions for cortex, subcortical GM, WM and CSf". What volume do I give 
the command as an input? T1, orig.mgz ‎. 
Best, 
Miracle

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Douglas N Greve‎
Sent: Thursday, January 26, 2017 5:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] White matter probability map.

ps, it is not a probability map per se but the volume fraction (0-1) map

On 01/26/2017 05:52 PM, Douglas N Greve wrote:
> Try mri_compute_volume_fractions
>
>
> On 01/26/2017 05:49 PM, miracoo...@gmail.com wrote:
>> Hello Freesurfer,
>> Is there a way to extract tissue probability map for white matter
>> in FS. Thank you
>> Best,
>> Miracle
>> Sent from my BlackBerry 10 smartphone.
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] White matter probability map.

2017-01-26 Thread Douglas N Greve

ps, it is not a probability map per se but the volume fraction (0-1) map


On 01/26/2017 05:52 PM, Douglas N Greve wrote:
> Try mri_compute_volume_fractions
>
>
> On 01/26/2017 05:49 PM, miracoo...@gmail.com wrote:
>> Hello Freesurfer,
>> Is there a way to extract tissue probability map for  white matter
>> in FS. Thank you
>> Best,
>> Miracle
>> Sent from my BlackBerry 10 smartphone.
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] White matter probability map.

2017-01-26 Thread miracooloz

 Hello Freesurfer, Is there a way to extract tissue probability map for  white matter   in FS. Thank you Best, Miracle Sent from my BlackBerry 10 smartphone.
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Re: [Freesurfer] Registration: Variable Must Begin with a Letter Error

2017-01-26 Thread Douglas N Greve

hi, please include previous correspondence so that we know what you are 
referring to

On 01/26/2017 04:10 PM, Anderson Napolitano wrote:
> Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces 
> and removing the spaces all together doesn't seem to resolve the said 
> error.
>
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Registration: Variable Must Begin with a Letter Error

2017-01-26 Thread Anderson Napolitano

?Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and 
removing the spaces all together doesn't seem to resolve the said error.

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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

2017-01-26 Thread Douglas Merkitch

Hello Lilla,

Thank you very much for the suggestion. Here then are my attempts at putting 
what you said into two sequential commands:

mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \
--m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --inv-morph \
--mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--o temporary_volume.mgz \
--interp trilin --no-save-reg

mri_vol2vol --targ temporary_volume.mgz \
--reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \
--inv \
--mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \
--o lowb.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg

Do the above commands look OK? I tried these commands, but the results were not 
great so I suspect that something is incorrect in the syntax and/or inputs.

Thanks for your help!

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu

On Jan 26, 2017, at 8:42 AM, Lilla Zollei 
>
 wrote:

Hi Doug,

In order to compute and apply the inverse of an m3z transform you would need to 
use the --inv-morph flag instead of the --m3z and reverse your targ and mov 
inputs. With the current implementation of mri_vol2vol though I do not think 
that you can specify the order of the transforms (which is important here), so 
you would need to apply the inverse non-linear trasform first and then the 
inverse rigid.

Lilla

On Wed, 25 Jan 2017, Douglas Merkitch wrote:

Hello Freesurfer experts,
>From your wiki page, I understand how to normalize volumes in subject 
>diffusion space to the CVS template:
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 $TUTORIAL_DIR/$subj/dtrecon/register.dat \
   --mov fa-masked.mgz \
   --o fa-masked.ANAT+CVS-to-avg35.mgz \
   --interp trilin --no-save-reg
However, how would one take take a volume in CVS template space and reverse 
normalize it back to subject diffusion space? Is this possible? If so, what 
would that command look like and what other st
eps would be necessary to get the required inputs?
Thanks,
Doug
Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Matlab Runtime

2017-01-26 Thread Iglesias Gonzalez, Eugenio

Ciao Stefano,
You have currently no permission to write in the FreeSurfer directory.
Try:
1. sudo -s
2. Enter your password
3. Run the curl and tar commands as explained in the wiki
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 26 Jan 2017, at 17:34, std...@virgilio.it wrote:

Hi list,
please see the error reported below.
Thanks
Stefano

curl
"http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2012bMAC.tar.gz;
-o "runtime2012b.tar.gz"
% Total% Received % Xferd Average Speed TimeTime Time Current
Dload Upload Total SpentLeft Speed
0 00 00 0 0 0 --:--:-- --:--:-- --:--:--
0Warning: Failed to create the file runtime2012b.tar.gz: Permission denied
0 290M0 9850 0 3211 0 26:23:33 --:--:-- 26:23:33 3208
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Re: [Freesurfer] surface based analysis

2017-01-26 Thread John Anderson

Thank you Doug,

Actually I was trying to apply what was mentioned in this link by replicating the method on  the command "mri_glmfit" and not  using the command "mri_mcsim".

 I tried to use for example the label "BA4a" (it is available in the folder/fsaverage/label), but the command "mriglm_fit failed to see it!! I ran the command as follow:

mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --label BA4a --glmdir lh

Kindly, what I am doing wrong in this command ? and how can I create label? What command I need? Can I use mri_binarize for example and save the output as a label?

John

Sent: Thursday, January 26, 2017 at 1:15 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis

FS does not come with correction tables for all labels. You'll have to
build your own. here are the instructions:

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

On 01/26/2017 01:09 PM, John Anderson wrote:
> Hello Freesurfers,
> I am working on a PET surface based analysis between two groups. I did
> the following:
> 1. I concatentaed the PET images using the command "mris_preproce"
> and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right
> hemisphere.
> 2. I smoothed "lh.mgh and rh.mgh) using the command:
> mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval
> lh_sm10.mgh
> 3. I studdied the diffence between the groups usiing the command:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --cortex --glmdir lh
> 4. I corrected the results for multiple comparison using the command:
> mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces
> I want to narrow (reduce the strictness) of the correction for
> multiple comparision to a specific label (e.g. precentral gyrus). I
> changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --label precentral --glmdir lh
> mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral
> --cwp 0.01 --2spaces
> I got error that the label "precentral" is not exist. I was unable to
> find this label in the folder "fsaverage". Kindly:
> 1. whct I am doing wrong?
> 2. How can I create this label ? and in whcih folder it must be placed?
> Best,
> John
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cortical volume from masked region

2017-01-26 Thread Eli Johnson

Ok sure, I will do it tomorrow as I don't have access to the stats file right 
now

Many thanks!


From: Eli Johnson 
Sent: Thursday, 26 January 2017 6:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region


Hi Doug,

Yes, I have a series of masks that I have created to cover the whole cortex, 
but I want to examine the regions separately. Each region outputs a volume much 
smaller than I would expect given the volumes from aseg stats for the whole 
cortex. That is to say, when I combine the volume from each region although I 
would expect it to be different to the volume from aseg stats (aseg stats is of 
course highly optimized), it's a lot smaller than expected - around half the 
size.

Sorry for not being more clear!
Thanks

> On 26 Jan 2017, at 18:11,y Douglas N Greve  wrote:
>
> In looking at your mask, it covers only half (or less) of the brain.
> This would explain why the total volume you get from the mask is much
> lesss than the total gm volume reported in aseg.stats.
>
>
>> On 01/20/2017 12:08 PM, Eli Johnson wrote:
>>
>> *Hi Doug,*
>>
>> *
>> *
>>
>> *Thanks a lot for your help!*
>>
>> *
>> *
>>
>> *I have run these commands and they complete with no problems. I can
>> also view the region overlaid on a surface and this looks ok, however
>> the volumes that are extracted from mri_segstats are much lower than
>> expected - around half the volume expected, and they don't seem in
>> line with the volumes automatically extracted (i.e. total cortical gm
>> volume from the aseg.stats file). Any thoughts on why this might be?*
>>
>> *
>> *
>>
>> *Many thanks!*
>>
>> *Eli
>> *
>>
>> *
>> *
>>
>> *
>> *
>>
>> *
>> *
>>
>> *Douglas N Greve*greve at nmr.mgh.harvard.edu
>> 
>> /Wed Jan 18 15:30:45 EST 2017/
>>
>>  * Previous message: [Freesurfer] Cortical volume from masked region
>>
>> 
>>  * Next message: [Freesurfer] installation fail :(
>>
>> 
>>  * *Messages sorted by:* [ date ]
>>
>> 
>>[ thread ]
>>
>> 
>>[ subject ]
>>
>> 
>>[ author ]
>>
>> 
>>
>>
>>
>> I would probably map the mask to the surface,eg,
>>
>> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i
>> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz
>>
>> The run
>>
>> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o
>> lh.vol.stats
>>
>>
>> 
>> *From:* Eli Johnson 
>> *Sent:* Tuesday, 17 January 2017 4:24 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Cortical volume from masked region
>>
>> Hi all,
>>
>>
>> I am trying to extract the volume from a FreeSurfer segmented scan
>> within a pre-registered mask region, but only within the cortex, and
>> wanted to check my command.
>>
>>
>> The mask is a binary mask (value of 1 across the mask) and is in the
>> same space as the orig.mgz file. It covers part of the frontal lobe.
>>
>>
>> I have run:
>>
>> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i
>> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum
>>
>>
>> This has output a text file with a value of 495563 mm3 in the last row.
>>
>>
>> I wanted to check whether this is the correct command to extract only
>> cortical GM within this mask. If this is correct, should be adding
>> other flags (e.g. -pv). I have searched the mailing list and the
>> options for mri_segstats, but I'm not 100% confident in what I've done
>> - so any tips would be greatly appreciated.
>>
>>
>> Many thanks
>> Eli
>>
>>
>>
>> ___
>> 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/
>
>

Re: [Freesurfer] Cortical volume from masked region

2017-01-26 Thread Douglas N Greve

In that case please upload the actual data that is failing.


On 01/26/2017 01:22 PM, Eli Johnson wrote:
> Hi Doug,
>
> Yes, I have a series of masks that I have created to cover the whole cortex, 
> but I want to examine the regions separately. Each region outputs a volume 
> much smaller than I would expect given the volumes from aseg stats for the 
> whole cortex. That is to say, when I combine the volume from each region 
> although I would expect it to be different to the volume from aseg stats 
> (aseg stats is of course highly optimized), it's a lot smaller than expected 
> - around half the size.
>
> Sorry for not being more clear!
> Thanks
>
>> On 26 Jan 2017, at 18:11,y Douglas N Greve  wrote:
>>
>> In looking at your mask, it covers only half (or less) of the brain.
>> This would explain why the total volume you get from the mask is much
>> lesss than the total gm volume reported in aseg.stats.
>>
>>
>>> On 01/20/2017 12:08 PM, Eli Johnson wrote:
>>>
>>> *Hi Doug,*
>>>
>>> *
>>> *
>>>
>>> *Thanks a lot for your help!*
>>>
>>> *
>>> *
>>>
>>> *I have run these commands and they complete with no problems. I can
>>> also view the region overlaid on a surface and this looks ok, however
>>> the volumes that are extracted from mri_segstats are much lower than
>>> expected - around half the volume expected, and they don't seem in
>>> line with the volumes automatically extracted (i.e. total cortical gm
>>> volume from the aseg.stats file). Any thoughts on why this might be?*
>>>
>>> *
>>> *
>>>
>>> *Many thanks!*
>>>
>>> *Eli
>>> *
>>>
>>> *
>>> *
>>>
>>> *
>>> *
>>>
>>> *
>>> *
>>>
>>> *Douglas N Greve*greve at nmr.mgh.harvard.edu
>>> 
>>> /Wed Jan 18 15:30:45 EST 2017/
>>>
>>>   * Previous message: [Freesurfer] Cortical volume from masked region
>>> 
>>> 
>>>   * Next message: [Freesurfer] installation fail :(
>>> 
>>> 
>>>   * *Messages sorted by:* [ date ]
>>> 
>>> 
>>> [ thread ]
>>> 
>>> 
>>> [ subject ]
>>> 
>>> 
>>> [ author ]
>>> 
>>> 
>>>
>>>
>>>
>>> I would probably map the mask to the surface,eg,
>>>
>>> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i
>>> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz
>>>
>>> The run
>>>
>>> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o
>>> lh.vol.stats
>>>
>>>
>>> 
>>> *From:* Eli Johnson 
>>> *Sent:* Tuesday, 17 January 2017 4:24 PM
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* Cortical volume from masked region
>>>
>>> Hi all,
>>>
>>>
>>> I am trying to extract the volume from a FreeSurfer segmented scan
>>> within a pre-registered mask region, but only within the cortex, and
>>> wanted to check my command.
>>>
>>>
>>> The mask is a binary mask (value of 1 across the mask) and is in the
>>> same space as the orig.mgz file. It covers part of the frontal lobe.
>>>
>>>
>>> I have run:
>>>
>>> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i
>>> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum
>>>
>>>
>>> This has output a text file with a value of 495563 mm3 in the last row.
>>>
>>>
>>> I wanted to check whether this is the correct command to extract only
>>> cortical GM within this mask. If this is correct, should be adding
>>> other flags (e.g. -pv). I have searched the mailing list and the
>>> options for mri_segstats, but I'm not 100% confident in what I've done
>>> - so any tips would be greatly appreciated.
>>>
>>>
>>> Many thanks
>>> Eli
>>>
>>>
>>>
>>> ___
>>> 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

Re: [Freesurfer] Cortical volume from masked region

2017-01-26 Thread Eli Johnson


Hi Doug,

Yes, I have a series of masks that I have created to cover the whole cortex, 
but I want to examine the regions separately. Each region outputs a volume much 
smaller than I would expect given the volumes from aseg stats for the whole 
cortex. That is to say, when I combine the volume from each region although I 
would expect it to be different to the volume from aseg stats (aseg stats is of 
course highly optimized), it's a lot smaller than expected - around half the 
size.

Sorry for not being more clear!
Thanks

> On 26 Jan 2017, at 18:11,y Douglas N Greve  wrote:
> 
> In looking at your mask, it covers only half (or less) of the brain. 
> This would explain why the total volume you get from the mask is much 
> lesss than the total gm volume reported in aseg.stats.
> 
> 
>> On 01/20/2017 12:08 PM, Eli Johnson wrote:
>> 
>> *Hi Doug,*
>> 
>> *
>> *
>> 
>> *Thanks a lot for your help!*
>> 
>> *
>> *
>> 
>> *I have run these commands and they complete with no problems. I can 
>> also view the region overlaid on a surface and this looks ok, however 
>> the volumes that are extracted from mri_segstats are much lower than 
>> expected - around half the volume expected, and they don't seem in 
>> line with the volumes automatically extracted (i.e. total cortical gm 
>> volume from the aseg.stats file). Any thoughts on why this might be?*
>> 
>> *
>> *
>> 
>> *Many thanks!*
>> 
>> *Eli
>> *
>> 
>> *
>> *
>> 
>> *
>> *
>> 
>> *
>> *
>> 
>> *Douglas N Greve*greve at nmr.mgh.harvard.edu 
>> 
>> /Wed Jan 18 15:30:45 EST 2017/
>> 
>>  * Previous message: [Freesurfer] Cortical volume from masked region
>>
>> 
>>  * Next message: [Freesurfer] installation fail :(
>>
>> 
>>  * *Messages sorted by:* [ date ]
>>
>> 
>>[ thread ]
>>
>> 
>>[ subject ]
>>
>> 
>>[ author ]
>>
>> 
>> 
>> 
>> 
>> I would probably map the mask to the surface,eg,
>> 
>> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i
>> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz
>> 
>> The run
>> 
>> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o
>> lh.vol.stats
>> 
>> 
>> 
>> *From:* Eli Johnson 
>> *Sent:* Tuesday, 17 January 2017 4:24 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Cortical volume from masked region
>> 
>> Hi all,
>> 
>> 
>> I am trying to extract the volume from a FreeSurfer segmented scan 
>> within a pre-registered mask region, but only within the cortex, and 
>> wanted to check my command.
>> 
>> 
>> The mask is a binary mask (value of 1 across the mask) and is in the 
>> same space as the orig.mgz file. It covers part of the frontal lobe.
>> 
>> 
>> I have run:
>> 
>> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i 
>> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum
>> 
>> 
>> This has output a text file with a value of 495563 mm3 in the last row.
>> 
>> 
>> I wanted to check whether this is the correct command to extract only 
>> cortical GM within this mask. If this is correct, should be adding 
>> other flags (e.g. -pv). I have searched the mailing list and the 
>> options for mri_segstats, but I'm not 100% confident in what I've done 
>> - so any tips would be greatly appreciated.
>> 
>> 
>> Many thanks
>> Eli
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error

Re: [Freesurfer] Surface space ICA

2017-01-26 Thread Douglas N Greve

Sorry, we don't have any tools to do ICA. The FSL/HCP group might have 
some thing that will do it on the surface.

On 01/26/2017 01:13 PM, David Baric Parker wrote:
> Hello!
>   I tried to look through the history but couldn't seem to find 
> exactly what I was looking for.
> Is there a recommended way to run ICA on vertex data?  For example, 
> I've transformed my raw fMRI data to surface space using fsfast, and 
> would like to extract group level IC's from this data.  Thanks!
> -David
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

___
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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.

Re: [Freesurfer] Cortical volume from masked region

2017-01-26 Thread Eli Johnson



Sent from my iPhone

> On 26 Jan 2017, at 18:11, Douglas N Greve  wrote:
> 
> In looking at your mask, it covers only half (or less) of the brain. 
> This would explain why the total volume you get from the mask is much 
> lesss than the total gm volume reported in aseg.stats.
> 
> 
>> On 01/20/2017 12:08 PM, Eli Johnson wrote:
>> 
>> *Hi Doug,*
>> 
>> *
>> *
>> 
>> *Thanks a lot for your help!*
>> 
>> *
>> *
>> 
>> *I have run these commands and they complete with no problems. I can 
>> also view the region overlaid on a surface and this looks ok, however 
>> the volumes that are extracted from mri_segstats are much lower than 
>> expected - around half the volume expected, and they don't seem in 
>> line with the volumes automatically extracted (i.e. total cortical gm 
>> volume from the aseg.stats file). Any thoughts on why this might be?*
>> 
>> *
>> *
>> 
>> *Many thanks!*
>> 
>> *Eli
>> *
>> 
>> *
>> *
>> 
>> *
>> *
>> 
>> *
>> *
>> 
>> *Douglas N Greve*greve at nmr.mgh.harvard.edu 
>> 
>> /Wed Jan 18 15:30:45 EST 2017/
>> 
>>  * Previous message: [Freesurfer] Cortical volume from masked region
>>
>> 
>>  * Next message: [Freesurfer] installation fail :(
>>
>> 
>>  * *Messages sorted by:* [ date ]
>>
>> 
>>[ thread ]
>>
>> 
>>[ subject ]
>>
>> 
>>[ author ]
>>
>> 
>> 
>> 
>> 
>> I would probably map the mask to the surface,eg,
>> 
>> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i
>> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz
>> 
>> The run
>> 
>> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o
>> lh.vol.stats
>> 
>> 
>> 
>> *From:* Eli Johnson 
>> *Sent:* Tuesday, 17 January 2017 4:24 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Cortical volume from masked region
>> 
>> Hi all,
>> 
>> 
>> I am trying to extract the volume from a FreeSurfer segmented scan 
>> within a pre-registered mask region, but only within the cortex, and 
>> wanted to check my command.
>> 
>> 
>> The mask is a binary mask (value of 1 across the mask) and is in the 
>> same space as the orig.mgz file. It covers part of the frontal lobe.
>> 
>> 
>> I have run:
>> 
>> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i 
>> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum
>> 
>> 
>> This has output a text file with a value of 495563 mm3 in the last row.
>> 
>> 
>> I wanted to check whether this is the correct command to extract only 
>> cortical GM within this mask. If this is correct, should be adding 
>> other flags (e.g. -pv). I have searched the mailing list and the 
>> options for mri_segstats, but I'm not 100% confident in what I've done 
>> - so any tips would be greatly appreciated.
>> 
>> 
>> Many thanks
>> Eli
>> 
>> 
>> 
>> ___
>> 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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> 
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> at
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Re: [Freesurfer] surface based analysis

2017-01-26 Thread Douglas N Greve

FS does not come with correction tables for all labels. You'll have to 
build your own. here are the instructions:

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


On 01/26/2017 01:09 PM, John Anderson wrote:
> Hello Freesurfers,
> I am working on a PET surface based analysis between two groups. I did 
> the following:
> 1. I concatentaed the PET images  using the command "mris_preproce" 
> and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right 
> hemisphere.
> 2. I smoothed "lh.mgh and rh.mgh) using the command:
> mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval 
> lh_sm10.mgh
> 3. I studdied the diffence between the groups usiing the command:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf 
> fsaverage lh --cortex --glmdir lh
> 4. I corrected the results for multiple comparison using the command:
> mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces
> I want to narrow (reduce the strictness) of the correction for 
> multiple comparision to a specific label (e.g. precentral gyrus). I 
> changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf 
> fsaverage lh --label precentral --glmdir lh
> mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral 
> --cwp 0.01 --2spaces
> I got error that the label "precentral" is not exist. I was unable to 
> find this label in the folder "fsaverage". Kindly:
> 1. whct I am doing wrong?
> 2. How can I create this label ? and in whcih folder it must be placed?
> Best,
> John
>
>
> ___
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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
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[Freesurfer] Surface space ICA

2017-01-26 Thread David Baric Parker

Hello!
  I tried to look through the history but couldn't seem to find exactly
what I was looking for.
Is there a recommended way to run ICA on vertex data?  For example, I've
transformed my raw fMRI data to surface space using fsfast, and would like
to extract group level IC's from this data.  Thanks!
-David
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Re: [Freesurfer] Cortical volume from masked region

2017-01-26 Thread Douglas N Greve

In looking at your mask, it covers only half (or less) of the brain. 
This would explain why the total volume you get from the mask is much 
lesss than the total gm volume reported in aseg.stats.


On 01/20/2017 12:08 PM, Eli Johnson wrote:
>
> *Hi Doug,*
>
> *
> *
>
> *Thanks a lot for your help!*
>
> *
> *
>
> *I have run these commands and they complete with no problems. I can 
> also view the region overlaid on a surface and this looks ok, however 
> the volumes that are extracted from mri_segstats are much lower than 
> expected - around half the volume expected, and they don't seem in 
> line with the volumes automatically extracted (i.e. total cortical gm 
> volume from the aseg.stats file). Any thoughts on why this might be?*
>
> *
> *
>
> *Many thanks!*
>
> *Eli
> *
>
> *
> *
>
> *
> *
>
> *
> *
>
> *Douglas N Greve*greve at nmr.mgh.harvard.edu 
> 
> /Wed Jan 18 15:30:45 EST 2017/
>
>   * Previous message: [Freesurfer] Cortical volume from masked region
> 
> 
>   * Next message: [Freesurfer] installation fail :(
> 
> 
>   * *Messages sorted by:* [ date ]
> 
> 
> [ thread ]
> 
> 
> [ subject ]
> 
> 
> [ author ]
> 
> 
>
>
>
> I would probably map the mask to the surface,eg,
>
> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i
> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz
>
> The run
>
> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o
> lh.vol.stats
>
>
> 
> *From:* Eli Johnson 
> *Sent:* Tuesday, 17 January 2017 4:24 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Cortical volume from masked region
>
> Hi all,
>
>
> I am trying to extract the volume from a FreeSurfer segmented scan 
> within a pre-registered mask region, but only within the cortex, and 
> wanted to check my command.
>
>
> The mask is a binary mask (value of 1 across the mask) and is in the 
> same space as the orig.mgz file. It covers part of the frontal lobe.
>
>
> I have run:
>
> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i 
> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum
>
>
> This has output a text file with a value of 495563 mm3 in the last row.
>
>
> I wanted to check whether this is the correct command to extract only 
> cortical GM within this mask. If this is correct, should be adding 
> other flags (e.g. -pv). I have searched the mailing list and the 
> options for mri_segstats, but I'm not 100% confident in what I've done 
> - so any tips would be greatly appreciated.
>
>
> Many thanks
> Eli
>
>
>
> ___
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> 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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[Freesurfer] surface based analysis

2017-01-26 Thread John Anderson

Hello Freesurfers,

I am working on a PET surface based analysis between two groups. I did the following:

1. I concatentaed the PET images using the command "mris_preproce" and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right hemisphere.

2. I smoothed "lh.mgh and rh.mgh) using the command:

mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval lh_sm10.mgh

3. I studdied the diffence between the groups usiing the command:

mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --cortex --glmdir lh

4. I corrected the results for multiple comparison using the command:

mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces

I want to narrow (reduce the strictness) of the correction for multiple comparision to a specific label (e.g. precentral gyrus). I changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow:

mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --label precentral --glmdir lh

mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral --cwp 0.01 --2spaces

I got error that the label "precentral" is not exist. I was unable to find this label in the folder "fsaverage". Kindly:

1. whct I am doing wrong?

2. How can I create this label ? and in whcih folder it must be placed?

Best,
John
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Re: [Freesurfer] Voxel intensities and aseg edits

2017-01-26 Thread Bruce Fischl


Hi Tamara

we don't use an intensity threshold as such. If you are looking for CSF, 
why not use our aseg and erode it once to avoid border voxels? Or twice if 
you want to be really certain.


I'll leave (2) for one of our longitudinal processing experts.

cheers
Bruce


On Thu, 26 Jan 2017, Tamara Tavares wrote:


Hello,

I have two questions which I was hoping to get some help with.

(1) I was wondering whether there was a intensity threshold for grey matter
and CSF. I know that Freesurfer scales the intensity so white matter has an
intensity of 110 (as can be seen at the bottom of Freeviewer when I open the
brianmask.mgz). I was wondering whether there is a threshold value I can use
to indicate whether a voxel is part of the CSF with 100% confidence?

(2) After I make edits to my aseg output in the longitudinal stream, do I
just run the following command to recreate the final volumes:

recon-long -autorecon2-noaseg -subjid 

I assume the -subjid is the name of the edited time point and 
is the name of the recreated volumes?

Thank you,
Tamara

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[Freesurfer] Matlab Runtime

2017-01-26 Thread stdp82

Hi list,please see the error reported below.ThanksStefano
curl 
"http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFiledo=gettarget=runtime2012bMAC.tar.gz;
 -o "runtime2012b.tar.gz"
  % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
  0 00 00 0  0  0 --:--:-- --:--:-- --:--:-- 
0Warning: Failed to create the file runtime2012b.tar.gz: Permission denied
  0  290M0   9850 0   3211  0 26:23:33 --:--:-- 26:23:33  3208 ___
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[Freesurfer] Voxel intensities and aseg edits

2017-01-26 Thread Tamara Tavares

Hello,

I have two questions which I was hoping to get some help with.

(1) I was wondering whether there was a intensity threshold for grey matter
and CSF. I know that Freesurfer scales the intensity so white matter has an
intensity of 110 (as can be seen at the bottom of Freeviewer when I open
the brianmask.mgz). I was wondering whether there is a threshold value I
can use to indicate whether a voxel is part of the CSF with 100% confidence?

(2) After I make edits to my aseg output in the longitudinal stream, do I
just run the following command to recreate the final volumes:

recon-long -autorecon2-noaseg -subjid 

I assume the -subjid is the name of the edited time point and  is the
name of the recreated volumes?

Thank you,
Tamara
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Re: [Freesurfer] freesurfer 6.0 with some of the analyses

2017-01-26 Thread Iglesias Gonzalez, Eugenio

Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That’s exactly my standard answer to that question ;-)

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 26 Jan 2017, at 15:55, Adam Martersteck 
> wrote:

I believe Dr. Iglesias previous responses on this exact question have been, 
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time 
having to download 2 different versions of freesurfer to achieve comparable 
results with your study.

I think the general consensus is "how many subjects do you have?" -- if it's 
less than 50, you may want to just rerun v6 on your subjects as it should 
preserve the edits -- but it's recommended you still open them up and double 
check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool 
> wrote:

Hi,

Can anyone comment on my question below?

I think the FAQ page mentions that the same version should be used to process 
all cases within a dataset, but my question is whether I can have the same 
dataset used for two different versions for separate analyses? This is 
considering that I've already

processed all my data with 5.3, but am interested in getting hippocampal 
subfields through 6.0.

Thanks so much!

Batool

From: Rizvi, Batool

Sent: Wednesday, January 25, 2017 12:54 PM

To: freesurfer@nmr.mgh.harvard.edu

Subject: freesurfer 6.0 with some of the analyses

Hi,

I'm wondering if it's okay to run some of the analyses within one study on 
v.5.3 and the other hippocampal analyses on 6.0?

Or do you recommend us starting over for the analyses we've already done in 5.3 
for that study?

Thank you!

Batool

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Re: [Freesurfer] freesurfer 6.0 with some of the analyses

2017-01-26 Thread Adam Martersteck

I believe Dr. Iglesias previous responses on this exact question have been,
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time
having to download 2 different versions of freesurfer to achieve comparable
results with your study.

I think the general consensus is "how many subjects do you have?" -- if
it's less than 50, you may want to just rerun v6 on your subjects as it
should preserve the edits -- but it's recommended you still open them up
and double check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool 
wrote:

>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
> Can anyone comment on my question below?
>
>
> I think the FAQ page mentions that the same version should be used to
> process all cases within a dataset, but my question is whether I can have
> the same dataset used for two different versions for separate analyses?
> This is considering that I've already
>
> processed all my data with 5.3, but am interested in getting hippocampal
> subfields through 6.0.
>
>
>
>
>
>
>
>
>
>
>
>
> Thanks so much!
>
>
> Batool
>
>
>
>
> --
>
>
> *From:* Rizvi, Batool
>
>
> *Sent:* Wednesday, January 25, 2017 12:54 PM
>
>
> *To:* freesurfer@nmr.mgh.harvard.edu
>
>
> *Subject:* freesurfer 6.0 with some of the analyses
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi,
>
>
> I'm wondering if it's okay to run some of the analyses within one study
> on v.5.3 and the other hippocampal analyses on 6.0?
>
> Or do you recommend us starting over for the analyses we've already done
> in 5.3 for that study?
>
>
>
>
>
>
> Thank you!
>
>
> Batool
>
>
>
>
>
>
>
>
>
>
> ___
>
> 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.
>
>
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Re: [Freesurfer] freesurfer 6.0 with some of the analyses

2017-01-26 Thread Rizvi, Batool

Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process 
all cases within a dataset, but my question is whether I can have the same 
dataset used for two different versions for separate analyses? This is 
considering that I've already processed all my data with 5.3, but am interested 
in getting hippocampal subfields through 6.0.


Thanks so much!
Batool

From: Rizvi, Batool
Sent: Wednesday, January 25, 2017 12:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freesurfer 6.0 with some of the analyses

Hi,
I'm wondering if it's okay to run some of the analyses within one study on 
v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us 
starting over for the analyses we've already done in 5.3 for that study?

Thank you!
Batool
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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs

2017-01-26 Thread Lilla Zollei



Hi Doug,

In order to compute and apply the inverse of an m3z transform you would 
need to use the --inv-morph flag instead of the --m3z and reverse your 
targ and mov inputs. With the current implementation of mri_vol2vol though 
I do not think that you can specify the order of the transforms (which is 
important here), so you would need to apply the inverse non-linear 
trasform first and then the inverse rigid.


Lilla

On Wed, 25 Jan 2017, Douglas Merkitch wrote:


Hello Freesurfer experts,
From your wiki page, I understand how to normalize volumes in subject diffusion 
space to the CVS template:

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 $TUTORIAL_DIR/$subj/dtrecon/register.dat \
--mov fa-masked.mgz \
--o fa-masked.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg

However, how would one take take a volume in CVS template space and reverse 
normalize it back to subject diffusion space? Is this possible? If so, what 
would that command look like and what other st
eps would be necessary to get the required inputs?

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu






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Re: [Freesurfer] longitudinal tracula error

2017-01-26 Thread Yendiki, Anastasia

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous

Re: [Freesurfer] Hippocampal Subfields Segmentation Error

2017-01-26 Thread Iglesias Gonzalez, Eugenio

I have never tried this. Does the rest of recon-all -all run without errors?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 25 Jan 2017, at 11:45, Michel Hu > wrote:

Dear  Juan,

I actually followed the guide on the following website in order to make it work 
on windows 10.
It seems to be a linux BASH shell with ubuntu 14.05.
http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/
Installing and running FreeSurfer on Windows 10 - Imaging 
...
nuclear-imaging.info
Before I get into how to install FreeSurfer, I must thank the author at K-Lab 
for the post on “How to run FSL on Windows 10“. That post describes how to 
install ...

Sincerely,
Michel hu




Van: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 namens Iglesias Gonzalez, Eugenio 
>
Verzonden: woensdag 25 januari 2017 12:30
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error

Dear Michel,
What exact platform are you using? Ubuntu 14.04 installed on a virtual machine 
running on Windows 10?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Jan 2017, at 12:47, Michel Hu > wrote:

Dear Freesurfer Developers,

For my research I'm trying to run the hippocampal subfield segmentation 
analysis however, I keep running into the following error. I tried to solve it 
by myself however I had no luck ( I tried by removing the exec flag from the 
files ).

I'm using the following sofftware
Freesurfer : freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Ubuntu: 14.04.5 LTS
WIndows 10

michel@-:~$ recon-all -s bob -hippocampal-subfields-T1
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r-- 1 michel 1590 1249629 Jan 24 13:40 
/usr/local/freesurfer/subjects/bob/scripts/recon-all.log
Linux - 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 
GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> 
'/usr/local/freesurfer/subjects/bob/scripts/recon-all.local-copy'
#
#@# Hippocampal Subfields processing (T1 only) left Tue Jan 24 13:43:46 STD 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects left

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument
#
#@# Hippocampal Subfields processing (T1 only) right Tue Jan 24 13:43:46 STD 
2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80 
/usr/local/freesurfer bob /usr/local/freesurfer/subjects right

See log file: 
/usr/local/freesurfer/subjects/bob/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML: error while 
loading shared libraries: libut.so: cannot enable executable stack as shared 
object requires: Invalid argument

Started at Tue Jan 24 13:43:45 STD 2017
Ended

[Freesurfer] Longitudinal stream with v6 but cross with v5.3

2017-01-26 Thread Matthieu Vanhoutte

Dear FS's experts,

I have run all my cross with v5.3 and hesitate to run all longitudinal
process with v6. Does that make sense and will improve the process or would
it be risky to do this ?

Many thanks for your lights !

Best regards,
Matthieu
___
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 tracula error

2017-01-26 Thread Bárbara Avelar Pereira

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

From the mailing list, it seems a similar issue has been fixed in previous 
updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

From what I understand, the base is not necessary to

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Re: [Freesurfer] longitudinal tracula error

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