Re: [Freesurfer] Tracula: missing or incomplete tracts

[Watson, Christopher]

What about:
freeview -v FA.nii.gz -v V1.nii.gz:vector=yes


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, March 17, 2015 11:57 AM
To: Freesurfer support list; Ruopeng Wang
Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts

Hi Amelia - Sorry, not that I know of. Perhaps this can be a feature
request for Ruopeng to add to freeview :)

BTW, freeview in 5.3 had a bug with the vector display for some input
image orientations, but this has been fixed in the dev version (that you
can download on the web site).

a.y

  On Thu, 12 Mar 2015, Versace, Amelia wrote:

> Dear Anastasia,
> I was wondering if there is a way to automatically (in command line) derive 
> the FA/V1 vector image.
> fslview FA.nii.gz V1.nii.gz   allows to load the FA and V1 image, but then 
> manual section of the (lines) is needed.
> freeview -dti V1 FA   does it too (with different xyz convention), 
> but the 'display as vectors' needs to be manually checked.
> Is there any way to produce this image using command line only? Thanks a 
> lot!! Amelia
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
> Sent: Friday, March 06, 2015 6:56 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts
>
>
> Hi Eileen - It looks like there was a A-P flip introduced to your gradient 
> vectors. (See screenshot of the tensor eigenvectors. Because they look right 
> in the coronal view but wrong in the sagittal and axial views, that's why I'm 
> assuming the flip is in the A-P direction.) To fix this you need to multiply 
> the y coordinate of your gradient vectors with -1 and rerun.
>
> If there are still any cases of missing tracts, please look at the bottom of 
> your dmrirc file for instructions on how to use the reinit parameter (or 
> search for previous emails on that parameter in the archives).
>
> Note that your DWI voxel size is anisotropic (finer resolution in x/y than 
> z), this may cause bias in tractography, so I'd recommend that you switch to 
> isotropic resolution for future acquisitions if you have control over it.
>
> Hope this helps,
> a.y
>
> On Fri, 27 Feb 2015, Eileen Moore wrote:
>
>> Hi Anastasia,
>>
>> Sorry for the delay -- I missed your response.  I did look at the
>> anatomical segmentations and thought they looked OK. I've uploaded the
>> tracula and corresponding freesurfer data for two subjects: one with 
>> complete tracts and one with missing/incomplete tracts. I also uploaded my 
>> dmrirc file. Thanks for taking a look for me.
>>
>> Eileen.
>>
>>
>>
>> Hi Eileen - Have you checked the anatomical segmentations of the
>> subjects? The mask that's used by default is the aparc+aseg_mask,
>> which comes from registering the cortical parcellationg and subcortical 
>> segmentation from T1 to diffusion space, and then dilating it by a couple of 
>> voxels.
>>
>> If you upload an example data set for me here, I can take a look:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2_&d=BQIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4&m=T2p7z8F4umjzf0YkkzlBSH_xnwrFLJ1rKFdoTAMUxbM&s=TVmCtWOX7TmzlQhiVJibKKVtj6CQczyAkyupGnmGZa0&e=
>> Please include all tracula-related directories of the subject (dmri, dlabel, 
>> etc).
>>
>> Thanks!
>> a.y
>>
>> On Thu, 18 Dec 2014, Eileen Moore wrote:
>>
>> Hi - I'm having difficulty with missing or incomplete tracts most of
>> my subjects. I'm hoping for suggestions on where I can look for data
>> problems.  The majority of my subjects have at least one
>> missing/incomplete tract, but the specific problematic tract varies
>> across subjects (e.g., one subject has a missing L.Uncinate; another
>> subject has a missing Forceps Major; another is missing the ILF
>> bilaterally, etc.).  For my problematic tracts, the path.pd.nii.gz is
>> a single line/curve rather than the diffuse volumetric distribution.
>> I'm not sure how to correct this.
>>
>> I have checked my eigenvectors -- the lines appear to be pointing in
>> the correct directions in my dtifit_V1 -- so I believe my gradient
>> table is correct
>>
>> I've checked my images for motion via visual inspection and by
>> excluding any subjects with dwi_motion outliers in AvgTranslation,
>> AvgRotation, PercentBadSlices, and AvgDropoutScore.
>>
>> I inspected the nodif_brain_mask.nii.gz  to look for chunks of missing
>> brain and did not identify any problems here.
>>
>> I've tried increasing the number of control points for each tract.
>>
>> I'd very much appreciate any suggestions on how to troubleshoot next.
>>
>> Thank you,
>> Eileen.
>>
>> ___
>> Freesurfer mail

Re: [Freesurfer] Freesurfer and Tracula installation.

[Watson, Christopher]

Have you tried these steps: http://wiki.centos.org/TipsAndTricks/NTFS

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fatma Zribi 
[zribi.fa...@gmail.com]
Sent: Thursday, April 23, 2015 9:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer and Tracula installation.

Hi everybody,

I installed CentOS 6.6 in a machine without using internet connexion. 
Everything is fine. I would like now to install Freesurfer and Tracula mounting 
a NTFS partition from an external hard disk. also I note that I can not copy 
Freesurfer in a FAT32 partition.

Actually I'm not sure that CentOs recognizes NTFS or FAT32 formats.

Please is there an expert who knows how to mount a NTFS disk using CentOS?

Thanks a lot for your help and your time.

Best regards,
Fatma

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Re: [Freesurfer] assigning 74 Destrieux parcellations into lobes, networks, sensory-motor modalities

[Watson, Christopher]

I have tools in R that can do #1, and network/graph theory analysis on top of 
that. I plan to work on things like #2-3 but haven't yet (e.g. there is 
possibly less consensus if region X is limbic vs. para-limbic, as opposed to 
temporal vs. parietal).
I can send you something in a few days/a week.

Although, If you read the Destrieux 2010 paper, you will see the regions (in 
the text) separated by lobe, at the least.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julie Evans 
[julie.evans.st...@gmail.com]
Sent: Thursday, July 23, 2015 11:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] assigning 74 Destrieux parcellations into lobes, 
networks, sensory-motor modalities

Dear FreeSurfer community,

I am a statistician who knows shamefully little about brain anatomy and I am 
writing with a request.

I don’t have easy access to Freesurfer and the original data but have the final 
text output i.e., the /stats folder, from a large cohort, which including 
*h.aparc.a2009s.stats.

I have been attempting to assign higher-order labels to the 74 Destrieux 
parcellations.

1) Categorizing uniquely into the 4 lobes: frontal, occipital, parietal, 
temporal;

2) Categorizing uniquely into “types of networks”: limbic, paralimbic, 
unimodal, heteromodal, subcortical, primary;

3) sensory-motor modality: somatosensory, visual, auditory, motor

As far as I understand these higher-order assignments of the 74 parcellations 
are not uncommon although not all cases are clear-cut so some knowledge of 
anatomy is needed (assuming that I am indeed looking at the correct level – 
gyri and sulci in the aparc.a2009s.stats file).

If so, would anyone mind sharing a text file with the correspondence between 
the 74 parcellations and lobes, network types, and/or modality?

I’d be very grateful for any guidance and help.

Thank you kindly,

J Evans
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Re: [Freesurfer] Huge difference ini area for the same subject {Disarmed}

[Watson, Christopher]

Doesn't that just mean your colleagues are editing the brains differently?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of amirhossein manzouri 
[a.h.manzo...@gmail.com]
Sent: Tuesday, July 28, 2015 7:33 AM
To: Douglas N Greve
Cc: free surfer
Subject: Re: [Freesurfer] Huge difference ini area for the same subject

Hi Doug,
As you can see in the image I attached the average area is different for the 
same set by two different editor. I wonder if there is any reason for this?

Best regards,
Amirhossein Manzouri




On Mon, Jul 27, 2015 at 9:16 PM, amirhossein manzouri 
mailto:a.h.manzo...@gmail.com>> wrote:
Hi Doug,
Yes, one set of subjects by two editors and no difference in thickness but huge 
difference on the area between two sets. Actually I want to see f there is any 
difference between editors for the same set of subjects.

On Monday, July 27, 2015, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
sorry, I'm not sure I understand. Can you elaborate what you did? Same set of 
subjects edited independtly by two editors? Then you look for a difference 
within the subjects and you don't find it with editor 1 but you do find it with 
editor 2?

On 07/27/2015 07:24 AM, amirhossein manzouri wrote:
Hi,
Two people has done recon-all and edits for the same subjects in FS version 5.1 
. In the qdec comparing same group which has been edited by two persons , we 
found no significant change in Cth but there is a pattern of area difference on 
both hemispheres showing significant decrease in middle area and increase on 
frontal and occipital. Do you have any idea what can be the reason for this?The 
first recon-all and edits and qcache have been done in 2012 and the second in 
2015! Attached is the sample screenshot.

Best regards,
Amirhossein Manzouri



--
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: 
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Re: [Freesurfer] Using FSL commands through Matlab (Linux)

[Watson, Christopher]

Just use either "system" or the exclamation mark and type the FSL commands


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Albrecht, Daniel S. 
[dsalbre...@mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using FSL commands through Matlab (Linux)

Hello,

Sorry if this isn’t the right forum for the question, but not sure where to 
direct it.

I’m trying to incorporate some FSL commands into a Matlab script. I’m using a 
Linux machine and running Matlab 7.11.0 (2010b). I tried to access the FSL 
toolbox through Matlab using:

setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
system(‘${FSLDIR}/etc/fslconf/fsl.sh’)

But received a “permissions denied” error. Is there an easier way to access FSL 
through Matlab?

Thanks,

Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging

Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.edu
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Re: [Freesurfer] Using FSL commands through Matlab (Linux)

[Watson, Christopher]

Ah, that's probably correct. I think it worked on my system because I source 
the FSL conf file in my .bashrc

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: Tuesday, August 04, 2015 4:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using FSL commands through Matlab (Linux)

I don't think that will work because the shell where FSLDIR gets set is
not the same shell as that of the system command. Try putting those two
in the same string and then running system on that


On 08/04/2015 04:36 PM, Albrecht, Daniel S. wrote:
> Hello,
>
> Sorry if this isn’t the right forum for the question, but not sure
> where to direct it.
>
> I’m trying to incorporate some FSL commands into a Matlab script. I’m
> using a Linux machine and running Matlab 7.11.0 (2010b). I tried to
> access the FSL toolbox through Matlab using:
>
> setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
> system(‘${FSLDIR}/etc/fslconf/fsl.sh’)
>
> But received a “permissions denied” error. Is there an easier way to
> access FSL through Matlab?
>
> Thanks,
>
> Daniel S. Albrecht, PhD
> Research Fellow in Radiology
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
> 149 Thirteenth Street, Room 2301
> Charlestown, MA 02129
> Phone: (617) 643-6748
> Fax: (617) 726-7422
> dsalbre...@mgh.harvard.edu
>   >
>
>
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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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4&m=MIxMSVH7VHFSDpQ8-QJrLgfoMt9e6HC2psPqEbMEK6I&s=lpz9t1_w9lORMfJLhdzVqC7oR6qHD21aZ5p5COeA9x8&e=
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: 
https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=BQIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4&m=MIxMSVH7VHFSDpQ8-QJrLgfoMt9e6HC2psPqEbMEK6I&s=3swWAORzQCwBZ2nupgWBHZtYtGCjZ06i7r2TrSrX0OE&e=

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Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

[Watson, Christopher]

Andre, I haven't done any statistical comparison, but for my data (pediatric) I 
found the DKT labels to be somewhat more accurate. The biggest differences were 
in superior frontal and rostral middle frontal. Other differences I've seen are 
anterior cingulate, cuneus, and fusiform. See Figure 4 in Klein & Tourville 
(2012).

RE your command example: have you tried including the full path for the images?
 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Son, Andre 
[andre@med.nyu.edu]
Sent: Sunday, August 09, 2015 11:41 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

Thank you Bruce.
You're alway so helpful, even on the weekend!

I'm also trying to convert mgz to nii and have been following various 
instructions online but can't seem to figure it out.

For ease, I  made a separate folder on the desktop with just mgz files in 
separate subject folders and ran the following commands verbatim:

mri_convert --in_type mgz --out_type nii --out_orientation RAS /mnt/ 
.../desktop/mgz/001/t1.mgz /mnt/ .../t1.nii.gz

I've also tried:
mri_convert /desktop/mgz/001/t1.mgz /desktop/mgz/001/t1.nii.gz

However, neither have worked, saying "mghRead(/desktop/mgz/001/t1.mgz, -1) 
could not open file"

Any suggestions?
Thank you.
AS
___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Sunday, August 09, 2015 11:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

Hi Andre

it's up to you. The aparc and .aparc.DKTatlas40 are probably pretty
similar, although we haven't looked at the .aparc.DKTatlas40 much. The
aparc.a2009s contains more, smaller parcels, and so is probably less
reliable but might correspond more closely to an anatomical hypothesis you
have.

cheers
Bruce

On Sun, 9 Aug 2015, Son, Andre wrote:

>
> Hello,
>
>
>
> What is the difference b/w the data generated in .aparc vs
> .aparc.DKTatlas40. vs. aparc.a2009s?
>
> Which data should I be using for studies on cortical thickness?
>
>
>
> Thank you,
>
> AS
>
>
>
>
>
>
> 
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>
>
>


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The informati

Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory

[Watson, Christopher]

I think it's a bit unclear what you're asking for. Have you followed the 
tutorials on the wiki? Can you post your directory structure?

What I do on my system is keep studies separate from one another. Each study 
directory has its own FS directory, and I keep the raw images separate. So 
something like the following:

.
|-- Study A
|-- DTI
|-- MPRAGE
|-- raw
|-- subj01
|-- subj01_mprage.nii.gz
|-- subj01_DICOMS
|-- subj02
|-- Freesurfer
|-- subj01
|-- subj02
|-- FMRI

...and so on



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Emma Thompson 
[vonecono...@gmail.com]
Sent: Monday, August 10, 2015 2:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] creating a new subject directory using imported data 
from existing subject directory
Hi,
I'm re-posting my query in case it got buried on the listserve:

Dear Freesurfers,
I created a single subject directory and then imported sdata from two separate 
studies, in the end I realized I should have created two subject directories 
and would like to now rectify the situation. My question is, 1) how do I create 
a second subject directory in a different location? and 2) how do I transfer my 
existing subjects' data from my current subject directory to this new subject 
directory without having to redo any of my work (surface reconstruction). Is 
this even possible at this point? Or is it that I should only have one FS 
directory after all and perhaps I should just move the location of this 
directory so it is more accessible for both of my studies? If this is the case, 
could you advise me on how to go about doing this?

BTW I'm using bash shell.
I hope my questions are clear. Thanks!!!
On Sat, Aug 8, 2015 at 1:24 PM, Emma Thompson 
mailto:vonecono...@gmail.com>> wrote:
Dear Freesurfers,
I created a single subject directory and then imported sdata from two separate 
studies, in the end I realized I should have created two subject directories 
and would like to now rectify the situation. My question is, 1) how do I create 
a second subject directory in a different location? and 2) how do I transfer my 
existing subjects' data from my current subject directory to this new subject 
directory without having to redo any of my work (surface reconstruction). Is 
this even possible at this point? Or is it that I should only have one FS 
directory after all and perhaps I should just move the location of this 
directory so it is more accessible for both of my studies? If this is the case, 
could you advise me on how to go about doing this?

BTW I'm using bash shell.
I hope my questions are clear. Thanks!!!
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Re: [Freesurfer] Computing SA from an older FS version

[Watson, Christopher]

1. Yes, I would expect that

2. Because the pial surface is bigger. (Unless I'm misunderstanding the 
question?)



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Gerrits, Niels 

Sent: Thursday, August 27, 2015 10:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version


Dear Experts,

With your help, I recalculated the surface area, now using the pial surface 
instead of the wm/gm boundary. I am, however, somewhat surprised by the 
discrepancy between my previous and current results, because the cortical 
surface area that is calculated using the pial is surface is consistently (a 
lot) larger than the SA that was calculated using the WM/GM boundary (please 
see below for an example). While computing the new SA measure, FS also 
automatically calculated both volume and thickness. Since these two measures 
are exactly the same as previously when SA was calculated using the wm/gm 
boundary (as was to be expected), I assume that the calculation of SA using the 
pial surface was correctly executed.

Nonetheless, I am wondering: 1) is such a large difference to be expected, and 
2) what could be a physiological explanation for this discrepancy?

All suggestions are much appreciated!

Best wishes,
Niels Gerrits




LH_cuneus_area

LH_entorhinal_area

LH_fusiform_area

LH_inferiorparietal_area

PP_01

1305

349

2563

3699

PP_02

1351

368

2989

4803

PP_03

1324

490

3489

3963

PP_04

1714

518

4107

4473

PP_05

1573

566

3750

5697

PP_06

1419

387

3206

4543

PP_07

1249

364

2636

4518

PP_08

1386

362

3174

5105

PP_09

1322

562

3239

6264

PP_10

1696

517

3926

5989













LH_cuneus_area

LH_entorhinal_area

LH_fusiform_area

LH_inferiorparietal_area

PP_01

1617

575

3231

4446

PP_02

1555

661

3970

5983

PP_03

1769

886

5059

5143

PP_04

1964

809

5402

5662

PP_05

1788

946

4832

6907

PP_06

1752

667

3944

5449

PP_07

1595

674

3631

5783

PP_08

1779

634

4074

6364

PP_09

1648

912

4353

7395

PP_10

1915

816

4758

7358






-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: maandag 13 juli 2015 14:46
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version



Hi Niels



the matlab commands should be:



>> [v, M,mr] = load_mgh('wm.mgz') ;

>> save_mgh(v, 'wm.mgz', M,mr);



cheers

Bruce

On Mon, 13 Jul 2015, Gerrits, Niels

wrote:



>

> Dear Bruce,

>

>

>

> Thanks for the quick reply! I think it might be possible that we used an

> unrelased or developmental version of FreeSurfer, because the building-stamp

> said: freesurfer-Linux-centos5_86_64_dev-20110315. I’m not sure how this

> version ended up onto the server I was working on. Do you think this is a

> problem?

>

>

>

> With respect to the error: you were right, it was longer. I copied the

> command line below:

>

>

>

> $ mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f

> stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c

> label/aparc.annot.ctab 0007 lh pial

> INFO: assuming MGZ format for volumes.

> INFO: using label/lh.cortex.label as mask to calc cortex NumVert, SurfArea

> and MeanThickness. computing statistics for each annotation in

> label/lh.aparc.annot. reading

> volume/data2/projects/ysbrand-vumc/pddatabase-freesurfer/niels_test//0007/mri/wm.

> mgz... znzTAGskip: tag=825050957, failed to calloc 1969843200 bytes!

>

>

>

> I then loaded wm.mgh into matlab and then saved it as you suggested and ran

> the command again to calculate SA of the pial surface, but it produces the

> exact same error…

>

>

>

> >> load.mgh wm.mgz;

>

> >> save.mgh wm.mgz;

>

>

>

> Am I doing anything wrong?

>

>

>

> Thanks again!

>

>

>

> Cheers,

>

> Niels

>

>

>

> -Original Message-

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

> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl

> Sent: zondag 12 juli 2015 16:44

> To: Freesurfer support list

> Subject: Re: [Freesurfer] Computing SA from an older FS version

>

>

>

> Hi Niels

>

>

>

> is that the entire error? Does it not say what volume produces the error?

>

> That was a bug we had briefly some time ago, but I didn't think it made it

>

> into anything we released.  If you can track down which volume is causing

>

> this problem you can just load it into matlab with load_mgh.m then save it

>

> with save_mgh.m and the error will go away (since the matlab code doesn't

>

> try to read or write the tagged information). Make sure to save all the

>

> volumes that you do this to somewhere before overwriting them.

>

>

>

> cheers

>

> Bruce

>

>

>

> On

>

> Sun, 12 Jul 2015, Gerrits, Niels wrote:

>

>

>

> > Dear FreeSurfer-experts,

>

> >

>

> > Unfortunately, nobody replied to my question so this is a repost (see the

>

> > orig

Re: [Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

[Watson, Christopher]

>From your original mail: I agree with Dr. Kanwisher. When you ask if it is 
>appropriate to "(visually) compare" list of regions, I would answer that it is 
>absolutely not. A direct comparison is necessary. See e.g. Nieuwenhuis et al., 
>2011, Nature Neuroscience.


For your second, I would say that it is not correct. Again, you should directly 
compare them. Otherwise, what are you basing the conclusion on? What effect 
size difference would you use as a cut-off between a "real" and "not real" 
difference? I think reading the above-mentioned paper will help with this 
question as well.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Francesco Puccettone 

Sent: Thursday, August 27, 2015 1:20 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Comparing lists of activated regions between 
task>ctrl contrasts

Sorry, forgot to add one additional (related) question:

is it ever correct to say "for region Y, the activations found for taskA were 
smaller than for taskB" just based on the two contrasts taskA>baseline and 
taskB>baseline? Or is it necessary that taskA and taskB be contrasted directly 
to be able to draw any conclusions (if any are sensible) about what 
smaller/larger activations of a certain region might mean?

Thanks!

On 27 August 2015 at 19:13, Francesco Puccettone 
mailto:francesco.puccett...@gmail.com>> wrote:
Hello all,

I have seen several (older) papers that draw conclusions about the implication 
of a brain region in a given task by using the following logic: region X was 
activated in the contrast taskA>baseline, but not in the contrast 
taskB>baseline; therefore, region X is implicated in/essential for the 
cognitive processes underlying taskA, but not also for that underlying taskB; 
in other words, it dissociates between the two tasks.

I believe Nancy Kanwisher addresses this point in a video lecture where she was 
pointing out that the above logic is flawed, and that said conclusion can only 
be drawn if the two tasks are contrasted directly (A>B). Have I understood this 
correctly, and does it ever make any sense to draw inferrences about implicated 
brain regions based on (visually) comparing the list of regions produced by 
contrasts comparing each task to the same baseline (in other words, by noticing 
which brain regions appear in one list, but not in the other)? Or, on the 
contrary, do all statistics and corrections need to be done voxel-wise, which 
is something that is only done when contrasting the two tasks directly?

Many thanks for any opinions.

--Francesco

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Re: [Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

[Watson, Christopher]

Yes, they are 2 separate atlases. The references are on the FS wiki.

The "ctab" files are colortable files, so I believe the "25 100 40 0" are the 
RGB + transparency/opacity


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of chenhf_uestc 
[chenhf_ue...@163.com]
Sent: Tuesday, September 29, 2015 10:59
To: freesurfer
Subject: [Freesurfer] Questions about the files of lh.aparc.stats and   
lh.aparc.DKTatlas40.stats

Dear Freesurfer experts,

In the stats folder of subject in the SUBJECTS_DIR, I found the files of 
lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results 
belong to two different atlas? Because the values and brain regions are 
different in these two files.

In these two files, I found the command "mris_anatomical_stats -mgz -cortex 
../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a 
../label/lh.aparc.annot -c ../label/aparc.annot.ctab NC058 lh white" and 
"mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab NC058 lh white".

So, the atlases are the lh.aparc.annot and lh.aparc.DKTatlas40.stats, 
respectively. Right?
However, when I open these two atlas (attached aparc.annot.ctab and 
aparc.annot.DKTatlas40.ctab), I found the contents are same. In addition, I 
would really want to know that the value in the aparc.annot.ctab. For ex.   1  
bankssts 25 100  400; what does the values mean? 25 100 40 0

Best,
Feng

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Re: [Freesurfer] aparc.DKTatlas40

[Watson, Christopher]

You can read about it here: 
http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2012.00171/abstract

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of krista kelly 
[krista.kell...@gmail.com]
Sent: Saturday, November 16, 2013 8:01 PM
To: freesurfer
Subject: [Freesurfer] aparc.DKTatlas40

I'm using freesurfer v. 5.3 and I see a new annotation, aparc.DKTatlas40.annot 
in the labels folder. Can anyone tell me what the difference between this and 
the apart.annot is? Does it just have 40 labels versus the 36 found in the 
older version?

Thanks!


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Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho

[Watson, Christopher]

I only have anecdotal evidence based on 4 subjects, but I found that using the 
FLAIR results in much better surface reconstruction than the multiecho. In my 
experience (with kids age 12-16), the pial surface was underestimated when I 
used the multiecho.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Saturday, December 14, 2013 1:10 PM
To: roberto.vivi...@uni-ulm.de
Cc: Andre van der Kouwe; Freesurfer@nmr.mgh.harvard.edu; eberhard.pra...@dzne.de
Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho

Hi Roberto

I think a T2-space FLAIR is your best bet. We have very little experience
with other FLAIR and/or/ T2s, but those seem to work well. They are *much*
higher SNR than the T2* maps that one can get from an memprage where the
last echo is only around 7ms.

cheers
Bruce
  On Sat, 14 Dec 2013,
roberto.vivi...@uni-ulm.de wrote:

> Dear all,
>
> starting from the version of March of this year, FreeSurfer supports
> the use of co-acquired FLAIR images to separate the dura from the gray
> matter. Some years ago, the idea about solving the same problem was to
> use multi-echo MPRAGE images. I am starting a new project, in which I
> am planning to acquire structural images, and I would like to know
> something more about these two ways of addressing the dura problem.
>
> -- is there any experience on the superiority of the FLAIR approach,
> or is there any published evaluation of it / comparison with the
> MEMPRAGE approach (such as the van der Kouwer et al. 2008 paper on the
> MEMPRAGE)  (I looked for it in scholar.google but could not find it)
>
> -- are you planning to support the multi echo approach in the future,
> or is it going to be discontinued
>
> I will also be very interested to hear from anyone who has had any
> experience with the FLAIR approach, or both.
>
> Best wishes,
> Roberto
>
> Roberto Viviani
> University of Ulm, Germany
>
>
>
> ___
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>
>
>
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Re: [Freesurfer] glmfit with correlated covariates

[Watson, Christopher]

I don't want to speak for the Freesurfer team, but I am 99% certain that it is 
Direct/Standard as you list them. There isn't any stepwise variable selection 
going on.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of L. Schweren 
[l.j.s.schwe...@umcg.nl]
Sent: Tuesday, March 25, 2014 6:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] glmfit with correlated covariates

Dear FreeSurfer experts,

Thank you for your fast reply. We are extracting cortical thickness values for 
statistical sub-analyses in SPSS (due to corrections required with regard to 
family relatedness within the data); therefore we want to be a 100% certain 
that the statistical model we use in SPSS is identical to the model used by 
mri_glmfit. Can you confirm that, out of the multiple linear regression types 
listed below, mri_glmfit makes use of the Direct (or Standard) regression model?

Type

Characteristics

Direct (or Standard)

· All IVs are entered simultaneously

Hierarchical

· IVs are entered in steps, i.e., some before others
· Interpret: R2 change, F change

Forward

· The software enters IVs one by one until there are no more 
significant IVs to be entered

Backward

· The software removes IVs one to one until there are no more 
non-significant IVs to removed

Stepwise

· A combination of Forward and Backward MLR


Thank you again for your help,

Best wishes,
Lizanne






Date: Wed, 12 Mar 2014 11:04:00 -0400

From: Douglas Greve 

Subject: Re: [Freesurfer] glmfit with correlated covariates

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <53207760.8010...@nmr.mgh.harvard.edu>

Content-Type: text/plain; charset="iso-8859-1"





It is just a standard multiple regression analysis where all regressors

are fit simultaneously. One weight does not include that of another weight.

doug





On 3/12/14 5:16 AM, L. Schweren wrote:

>

> Dear FreeSurfer experts,

>

> I am attempting to disentangle the effects of different features of

> pharmacological treatment on cortical thickness.

>

> I am running glmfit from the commandline, with multiple covariates

> (a.o. Z_Age, Z_TreatmentDuration and Z_StartAge) in the fsgd-file.

> These covariates are correlated up to approximately  0.6 , which to my

> understanding is not ideal yet not inducing collinearity. Running

> glmfit, I do not get any errors such as ill-designed matrix or so.

>

> My question regards the way the different regression weights are

> calculated in each voxel. If I test the variance in CT of voxel A

> explained by for example TreatmentDuration, and part of the variance

> in voxel A is explained by both TreatmentDuration and StartAge, will

> the regression weigth of TreatmentDuration than include the part that

> is also explained by StartAge? Or are all other covariates first

> "regressed out" of the variance, such that the variable I test can

> only explain the variance that was not explained by any of the other

> covariates?

>

> Thank you very much, your help is very much appreciated!

>

> Best wishes,

>

> Lizanne

>

>

>

> ___

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[Freesurfer] Graph theory analysis in R

[Watson, Christopher]

Dear Freesurfer users, (apologies for cross-post)

I am pleased to announce the release of an R package I created, called 
"brainGraph", for performing graph theory analyses of brain MRI data. You can 
use it for cortical thickness, volume, surface area, or LGI. It can also be 
used for tractography data (I have code that works with the outputs of FSL's 
"probtrackx2"), and it should work for resting-state fMRI as well. It is very 
heavily dependent on the fantastic R package "igraph" (see 
http://igraph.org/redirect.html). I created a GUI for quick and easy data 
exploration, but it isn't quite as polished as others out there (e.g., BrainNet 
Viewer).

For usage, please see the User Guide I put together (direct PDF link: 
https://www.dropbox.com/s/j831n3q9muyz1go/brainGraph_UserGuide.pdf?dl=0 ). You 
will find some code for getting your data into R, and I have documented many 
analysis steps and include multiple figures. I hope this is intuitive for both 
veteran and novice R users. Additionally, there are System Requirements, 
Installation instructions, and links for help learning R.

Some features that should be of interest include:
* bootstrapping & permutation testing
* random graph generation, small-worldness, and global/local/nodal efficiency
* rich-club calculations
* robustness ("targeted attack" or "random failure") & vulnerability: PDF of 
figure (PNG: https://www.dropbox.com/s/k14gdg1lomhh4l2/failPlot-1.pdf?dl=0)
* Plotting GUI - full GUI (PNG): 
https://www.dropbox.com/s/e0hdng7flrxsgd2/brainGraph_GUI.png?dl=0
* Plotting GUI - union of vertex neighborhoods (PNG): 
https://www.dropbox.com/s/aag5cn1p1z9xzxr/brainGraph_GUI_neighborhoods.png?dl=0
* Plotting GUI - community (module) plots (PNG): 
https://www.dropbox.com/s/8zzpd5j268qstmg/brainGraph_GUI_communities.png?dl=0

You can install it directly in R by typing: install.packages('brainGraph')
My Github page for the package (https://github.com/cwatson/brainGraph) contains 
the development version, and you can install that by typing: 
devtools::install_github('cwatson/brainGraph')
Please see the NEWS.md file 
(https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for updates made 
since the CRAN submission.
To work properly on Windows, you may need to install the devel version.

This is still a work-in-progress, so I am very happy to receive bug reports, 
feature requests, general coding help questions, (constructive) criticism, etc.
Please join the Google Group that I set up for those purposes:  
https://groups.google.com/forum/?hl=en#!forum/brainGraph-help


Chris Watson
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Re: [Freesurfer] Unknown option DKTatlas40

[Watson, Christopher]

The option should be:
--annot aparc.DKTatlas40

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman 
[marmaduke.wood...@univ-amu.fr]
Sent: Wednesday, March 2, 2016 08:27
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unknown option DKTatlas40

hi

I'm using the dev version of FreeSurfer on 64-bit Fedora 23.


Recon-all runs fine but at the end I see

$ recon-all -s tvb -aparc2aseg
...
  mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40

ERROR: Option --DKTatlas40 unknown


Running that command

$ mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos

without the --DKTatlas40 appears to run correctly.


Is this just an issue with the dev version or have I done something silly?


thanks,
Marmaduke


ps bugr output

FREESURFER_HOME: /opt/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160229

RedHat release: Fedora release 23 (Twenty Three)

Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64

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Re: [Freesurfer] pial surface with FLAIR

[Watson, Christopher]

Hi Veronica,
Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
And then, when you do the remaining recon-all steps:

recon-all -autorecon3 -s $SUBJECT -FLAIRpial

It has worked for me. (And worked very well! No edits necessary for the pial 
surface!)

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, April 15, 2013 12:31 PM
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] pial surface with FLAIR

Hi Veronica,

we haven't seen that before. Can you upload your subject including the
FLAIR and we'll take a look?

thanks
Bruce

On Mon, 15 Apr 2013, Popescu, Veronica wrote:

>
> Dear all,
>
> I have already run the FreeSurfer 5.2 -all, and I would like to improve the
> pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
> have also placed the FLAIR file) I use the following syntax:
>
> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>
> It starts running but then it hangs, I never get an output. The FLAIR file
> is in nifti format.
>
> I am not sure what I am doing wrong: it is the syntax? Should I first
> convert the FLAIR file to .mgz?
>
> Thank you in advance for the help!
>
> Veronica Popescu, MD, MSc
> Department of Radiology & Nuclear Medicine
> VU University Medical Center
> Amsterdam, The Netherlands
>
>

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Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

[Watson, Christopher]

I've never had any problems with sym links, but what you have is definitely 
confusing! Is there any reason you have it that way? As a rule of thumb, i'd 
keep things as simple as possible.

From: Garikoitz Lerma-Usabiaga [gariko...@gmail.com]
Sent: Saturday, June 01, 2013 4:21 PM
To: Watson, Christopher
Cc: Freesurfer
Subject: Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

Hello list,
we found the problem, symbolic links:

/home/glerma/ is the home of the app server where fs is installed.
/home/glerma/glerma/freesurfer/subjects was the SUBJECTS_DIR, but it has a sym 
link, since: glerma -> /bcbl/home/home_g-m/glerma
so changing SUBJECTS_DIR to:
/bcbl/home/home_g-m/glerma/freesurfer/subjects
solved the problem.


Do you think this is a problem with fs resolving sym links? We haven't found 
any problem with matlab or fsl.


thanks again!
Gari




On Sat, May 11, 2013 at 12:46 AM, Garikoitz Lerma-Usabiaga 
mailto:gariko...@gmail.com>> wrote:
Yes,
first two lines for example in SUBJECTS_DIR (I had to change SUBJECTS_DIR since 
now I have it in the app server, as said before):
drwxr-xr-x  77 glerma domain users  4096 Dec 20 17:25 BERTSO
drwxr-xr-x  10 glerma domain users  2048 Feb 14 16:27 BERTSO_MRI

and for the parent directory:
drwxr-xr-x  8 glerma domain users 1024 Mar 14 12:37 OSIRIX
drwxr-xr-x  8 glerma domain users 1024 Mar  8 08:59 OsiriX Data
drwxr-xr-x 26 glerma domain users 2048 May  7 17:55 subjects


thanks!
Gari



On Sat, May 11, 2013 at 12:37 AM, Chris Watson 
mailto:christopher.wat...@childrens.harvard.edu>>
 wrote:
Can you paste the output of "ls -l $SUBJECTS_DIR", so we can see what the 
permissions are? You may also want to paste the output of the parent directory 
as well.

On 05/10/2013 06:18 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Chris,
>  ls -l $SUBJECTS_DIR: it works
> This is the output of the command (I cannot make sense out of it):

[glerma@cajal ~]$ cat /etc/fstab
/dev/VolGroup00/LogVol00 /   ext3defaults1 1
LABEL=/boot /boot   ext3defaults1 2
tmpfs   /dev/shmtmpfs   defaults0 0
devpts  /dev/ptsdevpts  gid=5,mode=620  0 0
sysfs   /syssysfs   defaults0 0
proc/proc   procdefaults0 0
/dev/VolGroup00/LogVol01 swapswapdefaults0 0
/var/lib/swap/swap_cajal.img swap swap defaults 0 0
#hippocampus-nfs:/data /data nfs defaults 0 2
#hippocampus-nfs:/home/BCBL /home/BCBL nfs defaults 0 2
ltm.bcbl.local:/root_vdm_1/home /bcbl/home nfs4 defaults 0 0
ltm.bcbl.local:/root_vdm_1/data /bcbl/data nfs4 defaults 0 0

#hippocampus-nfs:/home/BCBL  /home/BCBL nfs 
rw,bg,intr,hard,timeo=600,wsize=32768,rsize=32768,nfsvers=3,tcp,noacl 0 2


(this is in the old app server, which worked before the migration to the new 
file system)

thanks again!
Gari


On Sat, May 11, 2013 at 12:07 AM, Chris Watson 
mailto:christopher.wat...@childrens.harvard.edu>>
 wrote:
Can you check that the UID and GID both match on the client and server sides? 
Is it the same user that is able to use other programs, yet unable to write via 
Freesurfer? Is your user an NIS account?

Can you output
# ls -l $SUBJECTS_DIR

I assume that since you say other programs can write to the filesystem, it is 
mounted properly, but can you show what is in /etc/fstab? i.e. make sure you 
see "rw" instead of "ro".


On 05/10/2013 05:55 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks for the answers.
I am not the sys admin, but I think I can answer both questions:
> I assume the system is in read-write mode since the rest of the programs 
> (i.e. Matlab) are working.
> The SUBJECT_DIR is in each personal space, I mean:
--- FS is installed in a Linux CentOS 5 machine, I have an account in that 
machine (and I can work normally if my SUBJECTS_DIR is in that machine)
--- I have a personal drive space in the NFS 4, and I used to have my 
SUBJECTS_DIR in that drive, but after they upgraded it to NFS 4, it didn't work 
again.
> We have a new cluster now, they are testing it, it has Red Hat installed, 
> with FS 5.2, and I've been told that it cannot write (same problem).

The strange thing is that other programs work fine with this setup.

Do you think the problem is in the file system config (it seems so) or in FS 
config to be able to work with NFS 4?

I have asked the sys admin for the output of the system-config-nfs, I don't 
have admin privileges to run it.

thanks again!
Gari



On Fri, May 10, 2013 at 11:46 PM, Nick Schmansky 
mailto:ni...@nmr.mgh.harvard.edu>> wrote:
Gari,

At the NMR Center we use NFS v4 without problems with freesurfer.  Is the
SUBJECTS_DIR writable?  Note that in the default freesurfer distribution,
th

Re: [Freesurfer] Painting voxels vs. adding control points

[Watson, Christopher]

1) The right panel shows the aseg voxels. The surfaces are the same in L and R 
panels.
2) What do the surrounding slices look like? It may be that the WM surface 
"fills in" more as you go along.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of ye tian 
[tianye...@gmail.com]
Sent: Thursday, July 04, 2013 11:52 AM
To: Freesurfer
Subject: Re: [Freesurfer] Painting voxels vs. adding control points

Dear Freesurfers,

My first attempt of this message somehow didn't make it to the mailing archive. 
In case it didn't go through, I am sending it again. Sorry to bother you if you 
received the first message.

Two things I was wondering
1) Why do the surfaces shown in the left and right panels disagree? (The right 
one has a lot more white matter).
2) Do I need to edit the white matter? It seems unreasonable to have +8mm thick 
of grey matter. If so, I will probably paint more voxels to wm.mgz.

Thank you very much!

Sincerely,
Ye


On Wed, Jul 3, 2013 at 4:33 PM, ye tian 
mailto:tianye...@gmail.com>> wrote:
Dear freesurfers,

I would like a second eye on my decision to edit wm.mgz. I think that the 
boundary between the gray and the white is unrealistic (e.g. Coronal.png). 
Furthermore, there is a discrepancy between -surfs and -surfs -aseg (e.g. 
attached coronal_aseg.png).

If I indeed need to edit these slices, which way is more preferable, adding 
voxels or control points?

Thank you very much!

Sincerely,
Ye


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Re: [Freesurfer] different results between 5.1.0 and 5.2.0

[Watson, Christopher]

I don't know, but I'm pretty sure the Freesurfer team will recommend you use 
v5.3.0. There are emails saying as much.
Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of clarissa yasuda 
[clayas...@gmail.com]
Sent: Thursday, July 25, 2013 12:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] different results between 5.1.0 and 5.2.0

Dear FreeSurfer Experts

As in some other posts, I have also observed some differences between the two 
releases.  The values from cuneus (thickness) are similar to the post from 
Ritobrato Datta, Ph.D. on 18 march.

 But I also observed some differences in volume of right / left thalami. Did 
anybody observe such asymmetry??
I am now running analysis with patients and controls on data from 5.2.0 and got 
surprised with this asymmetry.

Here I am showing the average I obtained:

R PALLIDUM  L PALLIDUM   R THAL L THAL  RH_CUNEUS   
LH_CUNEUS
5.1 (350 SUBJECTS)  15801688 6701   6970.31 1.845   1.857

5.2 (115 SUBJECTS, subgroup of 350) 151913676520
74012.422.40

Is there any approach to correct it on 5.2 ??
Thanks in advance
clarissa

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Re: [Freesurfer] trac-all inquiry

[Watson, Christopher]

I've found that when using the Bash shell, putting multiple subjects in the 
config file doesn't work. Maybe that's the issue here? Although, I simply never 
bothered to look into it any more.

Chris


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Soto 
[d.s...@imperial.ac.uk]
Sent: Friday, August 02, 2013 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all inquiry

Hi,

I have successfully run recon-all in my dataset
and now am attempting to use trac-all on my diffusion data
obtained on a Siemens scanner.

Diffusion dicoms were transformed to .nii using MRIConverter
and then to .mnc using

nii2mnc output.nii output_t.mnc.

I am trying to run trac-all on a single subject and for this I
have created the configuration file attached (tracula02ST)

As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
and within each subject the T1 serving as input for recon-all are in
mri/orig

while the diffusion images are in a folder call diffdata (named
output_t.mnc)
which also contains the bvecs and bvals files, which were transposed and
organised
according to the tutorial (named as bvecs_t.txt and bvals_t.txt)

When I run:
trac-all -c tracula02ST.txt

I get:
ERROR: no analysis step (-{prep,bedp,path}) has been selected

THEN I run:
trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so
and then gives the long output text below with an error message.

Segmentation fault (core dumped)
foreach: No match.

The trac-all.log is attached also.

Could you please help?

Cheers

David


--
http://www1.imperial.ac.uk/medicine/people/d.soto/






wmen-dsoto3:~/Documents/fmri/rsdtianawmgui> trac-all -prep -bedp -path
-c tracula02ST.txt
INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui
Actual FREESURFER_HOME /usr/local/freesurfer
trac-paths -c
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/dmrirc.local -log
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.log -cmd
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-paths
#-
#@# Path reconstruction Fri Aug  2 09:44:20 BST 2013
/usr/local/freesurfer/bin/dmri_paths --outdir
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cst_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cst_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ilf_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ilf_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.unc_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.unc_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fmajor_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fminor_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.atr_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.atr_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ccg_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ccg_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cab_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cab_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slfp_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slfp_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slft_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slft_PP_avg33_mni_bbr
--dwi /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz
--grad /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs --bval
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals --mask
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz
--bpdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri.bedpostX
--ntr 2 --fmin 0.05 --roi1
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni

Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

This is an FSL problem. You can try the FSL list, and check out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira 
[jbragapere...@gmail.com]
Sent: Monday, September 02, 2013 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Dear Anastasia and FreeSurfers,

I was preprocessing some data using tracula and found this error after running  
trac-all -bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
subjectdir is /data-02/joana/tracula/XXX/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Unable to run job: Job was rejected because job requests unknown queue 
"short.q".
Exiting.
Queuing parallel processing stage
Unable to run job: Job was rejected because job requests unknown queue "long.q".
Exiting.
Queuing post processing stage
Unable to run job: denied: "60" is not a valid object name (cannot start with a 
digit)
Job was rejected because job requests unknown queue "long.q".
Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the 
queued tasks.

You will get an email at the end of the post-processing stage.


So far no slices have been processed. Does anyone know how to solve it?

Thanks!

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Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

Indeed. It's actually really easy to set up, too.

From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL
customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

> This is an FSL problem. You can try the FSL list, and check out some links:
> https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
> http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira 
> [jbragapere...@gmail.com]
> Sent: Monday, September 02, 2013 9:53 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"
>
> Dear Anastasia and FreeSurfers,
>
> I was preprocessing some data using tracula and found this error after 
> running  trac-all -bedp -c dmrirc:
>
> INFO: SUBJECTS_DIR is /data-02/joana/Last
> INFO: Diffusion root is /data-02/joana/tracula/
> Actual FREESURFER_HOME /usr/local/freesurfer-5.3
> WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
> subjectdir is /data-02/joana/tracula/XXX/dmri
> Making bedpostx directory structure
> Queuing preprocessing stages
> Unable to run job: Job was rejected because job requests unknown queue 
> "short.q".
> Exiting.
> Queuing parallel processing stage
> Unable to run job: Job was rejected because job requests unknown queue 
> "long.q".
> Exiting.
> Queuing post processing stage
> Unable to run job: denied: "60" is not a valid object name (cannot start with 
> a digit)
> Job was rejected because job requests unknown queue "long.q".
> Exiting.
>
> Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
> Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the 
> queued tasks.
>
> You will get an email at the end of the post-processing stage.
>
>
> So far no slices have been processed. Does anyone know how to solve it?
>
> Thanks!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


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Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

A. You should overlay the tracts on the subject's FA (see example command line 
on wiki)
B. Check the mailing list archives about reinitializing tracts. That should 
improve the results here. You don't need to reinitialize the tracts that are 
already correct (although none of yours look particularly good).

Is this a noisy dataset or something?


From: Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Thursday, September 05, 2013 9:32 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi,

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize 
the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the 
tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently 
from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana




2013/9/2 Watson, Christopher 
mailto:christopher.wat...@childrens.harvard.edu>>
Indeed. It's actually really easy to set up, too.

From: Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL
customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

> This is an FSL problem. You can try the FSL list, and check out some links:
> https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
> http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
>
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  
> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>  on behalf of Joana Braga Pereira 
> [jbragapere...@gmail.com<mailto:jbragapere...@gmail.com>]
> Sent: Monday, September 02, 2013 9:53 AM
> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"
>
> Dear Anastasia and FreeSurfers,
>
> I was preprocessing some data using tracula and found this error after 
> running  trac-all -bedp -c dmrirc:
>
> INFO: SUBJECTS_DIR is /data-02/joana/Last
> INFO: Diffusion root is /data-02/joana/tracula/
> Actual FREESURFER_HOME /usr/local/freesurfer-5.3
> WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
> subjectdir is /data-02/joana/tracula/XXX/dmri
> Making bedpostx directory structure
> Queuing preprocessing stages
> Unable to run job: Job was rejected because job requests unknown queue 
> "short.q".
> Exiting.
> Queuing parallel processing stage
> Unable to run job: Job was rejected because job requests unknown queue 
> "long.q".
> Exiting.
> Queuing post processing stage
> Unable to run job: denied: "60" is not a valid object name (cannot start with 
> a digit)
> Job was rejected because job requests unknown queue "long.q".
> Exiting.
>
> Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
> Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the 
> queued tasks.
>
> You will get an email at the end of the post-processing stage.
>
>
> So far no slices have been processed. Does anyone know how to solve it?
>
> Thanks!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto: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
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Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

Try this: 
http://www.mail-archive.com/search?q=reinit&l=freesurfer%40nmr.mgh.harvard.edu

From: Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Thursday, September 05, 2013 9:51 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi Christopher,

Thanks a lot for such a prompt reply.

I know I should overlay the tracts of the FA image, but I just wanted to show 
you how small the reconsctrutions were.

I don't think this is particularly noisy data.

I'm trying to find solutions on the mailing list archives by typing 
"reinitializing tracts Tracula" but I haven't found much information.

Would you kindly suggest me a few that provide solutions to this problem or 
make some recommendations yourself?

Thanks again,

joana




2013/9/5 Watson, Christopher 
mailto:christopher.wat...@childrens.harvard.edu>>
A. You should overlay the tracts on the subject's FA (see example command line 
on wiki)
B. Check the mailing list archives about reinitializing tracts. That should 
improve the results here. You don't need to reinitialize the tracts that are 
already correct (although none of yours look particularly good).

Is this a noisy dataset or something?


From: Joana Braga Pereira 
[jbragapere...@gmail.com<mailto:jbragapere...@gmail.com>]
Sent: Thursday, September 05, 2013 9:32 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi,

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize 
the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the 
tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently 
from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana




2013/9/2 Watson, Christopher 
mailto:christopher.wat...@childrens.harvard.edu><mailto:christopher.wat...@childrens.harvard.edu<mailto:christopher.wat...@childrens.harvard.edu>>>
Indeed. It's actually really easy to set up, too.

From: Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu><mailto:ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>>]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL
customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

> This is an FSL problem. You can try the FSL list, and check out some links:
> https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
> http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
>
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>  
> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>]
>  on behalf of Joana Braga Pereira 
> [jbragapere...@gmail.com<mailto:jbragapere...@gmail.com><mailto:jbragapere...@gmail.com<mailto:jbragapere...@gmail.com>>]
> Sent: Monday, September 02, 2013 9:53 AM
> To: 
> freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"
>
> Dear Anastasia and FreeSurfers,
>
> I was preprocessing some data using tracula and found this error after 
> running  trac-all -bedp -c dmrirc:
>
> INFO: SUBJECTS_DIR is /data-02/joana/Last
> INFO: Diffusion root is /data-02/joana/tracula/
> Actual FREESURFER_HOME /usr/local/freesurfer-5.3
> WARN: Ru

Re: [Freesurfer] tool to compare surface files (along the lines of diff)?

[Watson, Christopher]

You could probably load them in matlab and compare there.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Romano 
[drom...@stanford.edu]
Sent: Thursday, September 05, 2013 8:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] tool to compare surface files (along the lines of diff)?

Hi everyone,

I'm trying to figure out whether two surfaces which appear identical in 
freeview are indeed identical. Using diff shows the files are not, but since 
they're binary, I can't tell whether this difference is simply due to header 
information that might be embedded in the files, or whether the surfaces do 
indeed differ.   Is there a FreeSurfer command that can be used to determine 
this?

Thanks in advance for your help,
David Romano

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

Re: [Freesurfer] recon-all for multiple subjects

[Watson, Christopher]

The problem here is that SZ*.nii presumably refers to a list of files due to 
shell expansion. I don't know how recon-all handles that (e.g. if it will take 
only the first file in the list, or all files), but that command probably won't 
do what you want it to.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anupa AV 
[av.an...@yahoo.com]
Sent: Saturday, September 07, 2013 5:56 AM
To: KOOL; Freesurfer
Subject: [Freesurfer] recon-all for multiple subjects

Dear Sir,
I'd like to know the command lines for running recon-all for multiple datasets.
Can you please help me on that?

I've tried using the following command lines

cd /home/john/Anu (where I kept all the .nii files)

for x in *
do
recon-all -i SZ*.nii -s $x -all
done

But this is not working

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] MPRAGE intensity variations

[Watson, Christopher]

I'll look into it. I doubt it's been used for the previous scans.
Given that, is there anything I can do (any flags/options to declare) that can 
deal with this kind of issue? I don't mind adding control points and whatnot, 
but an easy fix is obviously desirable.

Thanks,
Chris

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Saturday, July 14, 2012 5:29 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE intensity variations

Hi Chris
Are you using prescan normalize? It helps a lot
Cheers
Bruce



On Jul 13, 2012, at 1:00 PM, Chris Watson 
mailto:christopher.wat...@childrens.harvard.edu>>
 wrote:

Hello,
I ran a subject through recon-all both with and without the "-mprage" flag, and 
naturally got different results. I'm attaching a screenshot of the pial and 
main surfaces, along with the orig.mgz of the same slice. The image tends to be 
brighter in the frontal lobe, and there is an intensity change when going 
through the slices. The scanner is Siemens 3T (Trio, I think), using a 
32-channel head coil. The imaging parameters are: (not sure which are most 
relevant)

TR: 1410
TI: 800
TE: 2.2
Matrix: 256x256
FOV: 256
Flip angle: 9 deg
ImagingFrequency: 123.259181
Pixel bandwidth: 199

Is there anything I can do to improve the results?
Thanks,
Chris

PS When I didn't use the '-mprage' flag, I used the '-nuintensitycor-3T' flag. 
So I changed 2 separate things.



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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

[Watson, Christopher]

Hi Doug et al,

The 2nd question is something I've wondered about. Doesn't a Bonferroni 
correction assume that the measures are independent? 
If so, I think in the case of subcortical structures, it is incorrect to use 
this method, as e.g. the putamen and pallidal volumes are not independent of 
one another.
If not, and it is acceptable to use when there are dependencies between 
measures, how do you calculate the FWE? It wouldn't be equal to alpha/n, unless 
I am misunderstanding something.

Thanks,
Chris

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, July 20, 2012 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

Hi Reem, it looks like you've done everything correctly (sorry for the
null result). As for your second, question, I don't think there is a way
other than Bonferroni. You can try FDR, but it makes the interpretation
a little messy.
doug

On 07/19/2012 07:59 PM, Reem Jan wrote:
>
> Hi Doug
>
> I hope it’s okay that I double check I’m doing the correction over 2
> hemispheres correctly and ask a question regarding correction for
> multiple comparisons. I will briefly describe what I have done:
>
> I have 2 groups of subjects – Drug addicts (n= 17) and controls (n=20).
>
> 1.I ran a surface thickness study:
>
> ·For the ‘mri_glmfit’ command, I used DOSS and specified a contrast of
> +1 -1 0 (Controls > MA)
>
> ·I ran a pre-cached simulation with the following command:
> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>
> ·This simulation should only have corrected for the left hemisphere as
> I understand it. My cluster summary text file showed me that a cluster
> survived in the insula. I interpreted this as ‘controls had higher
> grey matter thickness in this cluster located in the insula than drug
> addicts’. However, this was only corrected over the left hemisphere
> (when I ran the same simulation in the right hemisphere, nothing
> survived multiple comparison correction).
>
> ·I now wanted to correct the lh results for 2 hemispheres. From the
> help menu of ‘mri_glmfit-sim’, I understood you can do this in 2 ways,
> are both of these correct and give the same result?
>
> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 spaces
> --no-sim csdbase
>
> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
> --cwpvalthresh 0.025
>
> ØNo clusters survived the Bonferroni correction over both hemispheres.
> So I assume I can no longer report this result?
>
> 2.I ran a subcortical volume study:
>
> ·I used SPSS to perform the statistical analysis on each of 14
> subcortical structures (left and right). Is there a good way to
> correct for multiple comparisons, apart from Bonferroni, which would
> be very conservative?
>
> Many thanks for your advice.
>
> Kind regards
>
> Reem
>
> *Reem Jan***
>
> BPharm (Hons), RegPharmNZ
>
> PhD Student / Pharmacist
>
> School of Pharmacy, Faculty of Medical & Health Sciences,
> The University of Auckland, Private Bag 92019,
> Auckland, New Zealand.
>
> Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138
>
> F: +64 9 367 7192
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas
> Greve
> *Sent:* Friday, 20 July 2012 11:52 a.m.
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] slice-by-slice predictors
>
> Sorry, not possible.
>
> On 7/19/12 6:56 PM, Caspar M. Schwiedrzik wrote:
>
> Hi!
> Is it possible to have slice-by-slice predictors in Freesurfer, and if
> so, how?
> Thanks,
> Caspar
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu  
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

[Watson, Christopher]

What about, for example, the correlations I've seen in a cohort of subjects.

In 158 subjects aged 10-19 (both controls and patients), the correlation 
between L & R thalamus is 0.91, and the correlations between L & R of caudate, 
putamen, pallidum, hippocampus, and amygdala were all 0.75 or higher.

I would think that a Bonferroni correction would be incredibly conservative 
and, in my opinion, just plain wrong because true significant diff's would be 
missed. Is there any principled way of dealing with multiple tests that are 
correlated?

Thanks,
Chris

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Saturday, July 21, 2012 12:01 PM
To: Watson, Christopher
Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

Hi Chris,

bonferroni will be overly conservative in that case, but we rarely really
know the true covariance structure of the data, so we would rather err on
the side of being conservative.

cheers
Bruce
On Fri, 20 Jul 2012, Watson, Christopher
wrote:

> Hi Doug et al,
>
> The 2nd question is something I've wondered about. Doesn't a Bonferroni 
> correction assume that the measures are independent?
> If so, I think in the case of subcortical structures, it is incorrect to use 
> this method, as e.g. the putamen and pallidal volumes are not independent of 
> one another.
> If not, and it is acceptable to use when there are dependencies between 
> measures, how do you calculate the FWE? It wouldn't be equal to alpha/n, 
> unless I am misunderstanding something.
>
> Thanks,
> Chris
> 
> 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, July 20, 2012 2:38 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and 
> MCC
>
> Hi Reem, it looks like you've done everything correctly (sorry for the
> null result). As for your second, question, I don't think there is a way
> other than Bonferroni. You can try FDR, but it makes the interpretation
> a little messy.
> doug
>
> On 07/19/2012 07:59 PM, Reem Jan wrote:
>>
>> Hi Doug
>>
>> I hope it?s okay that I double check I?m doing the correction over 2
>> hemispheres correctly and ask a question regarding correction for
>> multiple comparisons. I will briefly describe what I have done:
>>
>> I have 2 groups of subjects ? Drug addicts (n= 17) and controls (n=20).
>>
>> 1.I ran a surface thickness study:
>>
>> ·For the ?mri_glmfit? command, I used DOSS and specified a contrast of
>> +1 -1 0 (Controls > MA)
>>
>> ·I ran a pre-cached simulation with the following command:
>> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>>
>> ·This simulation should only have corrected for the left hemisphere as
>> I understand it. My cluster summary text file showed me that a cluster
>> survived in the insula. I interpreted this as ?controls had higher
>> grey matter thickness in this cluster located in the insula than drug
>> addicts?. However, this was only corrected over the left hemisphere
>> (when I ran the same simulation in the right hemisphere, nothing
>> survived multiple comparison correction).
>>
>> ·I now wanted to correct the lh results for 2 hemispheres. From the
>> help menu of ?mri_glmfit-sim?, I understood you can do this in 2 ways,
>> are both of these correct and give the same result?
>>
>> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 spaces
>> --no-sim csdbase
>>
>> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>> --cwpvalthresh 0.025
>>
>> ØNo clusters survived the Bonferroni correction over both hemispheres.
>> So I assume I can no longer report this result?
>>
>> 2.I ran a subcortical volume study:
>>
>> ·I used SPSS to perform the statistical analysis on each of 14
>> subcortical structures (left and right). Is there a good way to
>> correct for multiple comparisons, apart from Bonferroni, which would
>> be very conservative?
>>
>> Many thanks for your advice.
>>
>> Kind regards
>>
>> Reem
>>
>> *Reem Jan***
>>
>> BPharm (Hons), RegPharmNZ
>>
>> PhD Student / Pharmacist
>>
>> School of Pharmacy, Faculty of Medical & Health Sciences,
>> The University of Auckland, Private Bag 92019,
>> Auckland, New Zealand.
>>
>> Ph: +64 9 373 7599 ext 81138. DDI: +64

Re: [Freesurfer] TRACULA -prep error

[Watson, Christopher]

I've just taken to making the sym links myself after running trac-prep and 
before running bedpostx. Then everything should run normally.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, August 16, 2012 4:24 PM
To: Richard Binney
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA -prep error

Hi Richard - In the listing you sent below I do see the a
nodif_brain_mask.nii.gz and a control.dat, although I have no idea what
control.dat is. As for data.nii.gz, it should be created as a symbolic
link to dwi.nii.gz, since bedpostx indeed expects it to be called "data".
I have not seen this problem before, but does it occur only when you rerun
and overwrite things in the same directory, or also when you start a fresh
run on a previously non-existent directory?

a.y

On Thu, 16 Aug 2012, Richard Binney wrote:

> Hi Anastasia et al.,
>
> I previously had TRACULA running wonderfully on a test dataset. I was tasked
> with writing an in-house step-by-step manual for dummies. Since then, a
> colleague has followed my manual with a new dataset and had problems. After
> trying to determine whether it was her install or something about her data
> and failing to find anything, I returned to re-run the subject I had already
> successfully processed. Nothing has changed in my install (TRAC-all version
> etc) ODDLY, this re-run is suffering from the same problem as my colleague.
>
> We ran trac-all -prep -dmrirc and it exited without any errors. However,
> there seem to be some files missing from the output:
>
> control.dat
>
> data.nii.gz
>
> nodif_brain_mask.nii.gz
>
>
>
> Bedpostx will not run due to the data file being missing and I'm sure the
> other missing files will cause problems.
>
> What is going on?
>
> I knew to look for these files as at some point I found the following list
> for the \dmri\. I can not re-find a post with this list so I'm sorry if it
> related to a solution to our current problem.
>
> Please help
>
> Richard
>
> brain_anat_mni.nii.gz
>
> dtifit_L2.nii.gz  dwi_orig_flip.nii.gz
>
> brain_anat.nii.gz
>
> dtifit_L3.nii.gz
>
> dwi_orig.mghdti.bvals
>
> brain_anat_orig.nii.gz  dtifit_MD.nii.gz
>
> dwi_orig.mghdti.bvecs
>
> bvals
>
> dtifit_MO.nii.gz  dwi_orig.nii.gz
>
> bvecs
>
> dtifit_S0.nii.gz  dwi_snr.txt
>
> bvecs.norot
>
> dtifit_V1.nii.gz  lowb_brain.nii.gz
>
> control.dat
>
> dtifit_V2.nii.gz
>
> lowb.nii.gz
>
> data.nii.gz
>
> dtifit_V3.nii.gz
>
> mni
>
> dtifit_FA.nii.gz
>
> dwi.ecclog
>
> nodif_brain_mask.nii.gz
>
> dtifit_L1.nii.gz
>
> dwi.nii.gz
>
>  xfms
>
>
>
>

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Re: [Freesurfer] TRACULA some fiber volumes being too small

[Watson, Christopher]

There were recently a few messages on the list regarding this.
What you should do is include "set reinit=1" in your config file, and then run
trac-all -priors -c $CONFIG
trac-all -path -c $CONFIG

Make sure you only include the pathway of interest in the config file; 
otherwise, it will re-run the analysis for all 18.
That has worked for me most of the time.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fernando Ventrice 
[fventr...@fleni.org.ar]
Sent: Thursday, October 18, 2012 10:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FW: TRACULA some fiber volumes being too small

Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what it can 
do automatically. These are the commands I used:

export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
 -v 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
 &

All finished without errors, but there seems to be a problem with CC Forceps 
Mayor volume, which gave very small values. Is this OK or I made some mistake? 
First I tested with some patient and other fiber tracks also gave very small 
volumes. I attached some pictures and the dmrirc and trac-all log files.
Best,
Fernando Ventrice

El contenido del presente mensaje y el de sus adjuntos, es confidencial, 
privado y de uso exclusivo de los destinatarios a los cuales está dirigido, 
pudiendo contener información legalmente protegida. Queda prohibida la 
revisión, divulgación, publicación, modificación, copia, distribución o acción 
en relación con esta información, por personas o entidades distintas al 
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor 
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son 
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar

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Re: [Freesurfer] Red Hat Enterprise Linux 6?

[Watson, Christopher]

I've had no problems with it.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Brain Apprentice 
[bapprent...@gmail.com]
Sent: Tuesday, November 20, 2012 11:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Red Hat Enterprise Linux 6?

Hi Surfers,

I was wondering if FreeSurfer v5.1.0 (CentOS 4 x86 (64b)) or V5.X will work on 
Red Hat Enterprise Linux 6?

The reason I ask is that the supercomputer at Brigham Young University is going 
through a major overhaul: changing the OS, adding more nodes, and adding more 
storage.

I am just curious what type of problems I will run into. I know I will need to 
rerun all brains through the new system but more concerning to me is if I can 
run FreeSurfer at all on the new system.

Thanks in advance for any suggestions or insights you can offer.



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Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Watson, Christopher]

Hi Bruce,
So would you recommend acquiring a T2 in addition to an (ME)MPRAGE/SPGR? i.e. 
is it worth squeezing another acquisition into a protocol?

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, November 20, 2012 3:01 PM
To: Winter, Warren
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface 
recons?

Hi Warren

yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
will use either a FLAIR or T2 (ideally T2-SPACE for either one)

cheers
Bruce
On Tue, 20
Nov 2012, Winter, Warren wrote:

> Hi all,
>
> Back in January and October Bruce mentioned that he had under development 
> some scripts designed to utilize T2-SPACE images for better pial surface 
> reconstruction in the presence of dura -- I was just wondering if any of that 
> is ready for trial?
>
> Thanks!
>
> Warren
>
> --
> Warren Winter
> Research Coordinator
> Boston Children's Hospital
> Sheridan Laboratory of Cognitive Neuroscience
> Division of Developmental Medicine
> 1 Autumn Street, AU 650
> Boston, MA 02215
> 857-218-5224
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Cortical thickness analysis on data acquired from multiple sites

[Watson, Christopher]

Hi Bruce,
What if she created an FSGD file, and instead of just having "patients" and 
"controls", she would have "patients1.5", "patients3", etc.? With over 400 
subjects this should be feasible, i.e. the loss of d.f. is worth running the 
combined analysis.

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, February 18, 2013 10:59 AM
To: Jorge Jovicich
Cc: Sinead Kelly; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Cortical thickness analysis on data acquired from 
multiple sites

Hi Sinead

I agree with Jorge - there is bound to be a substantial scanner effect. You
might be better off keeping the data separate and treating the 3T as a
confirmatory study.

cheers
Bruce



On
Mon, 18 Feb 2013, Jorge Jovicich wrote:

> Dear Sinead,
>
> we found global significant differences in thickness between 1.5T and
> 3T, in a group of subjects that was scanned at both scanners
> (http://www.ncbi.nlm.nih.gov/pubmed/16651008). I think that nothing
> stops you from doing the analysis, but maybe model in a field effect to
> asset it in your own data.
>
> Cheers,
>
> jorge
>
>
> On 18/02/2013 16:32, Sinead Kelly wrote:
>> Dear members,
>>
>> I would like to get your opinion on this issue - I have a dataset of
>> over 400 subjects but under half of this data was acquired on a 1.5T
>> scanner and the rest was acquired on a 3T scanner. Would it be
>> acceptable to conduct cortical thickness analysis on the combined
>> dataset? From reading the literature it seems that this is not a major
>> problem but I just wanted to get some more thoughts on this.
>>
>> Thank you for your help,
>>
>> Sinead
>>
>> --
>> Sinead Kelly
>> Neuropsychiatric Genetics Group
>> Trinity Centre
>> St. James's Hospital
>> Dublin 8
>
>
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Re: [Freesurfer] GLM: What's the link?

[Watson, Christopher]

In this case, GLM stands for "General Linear Model", and not "Generalized 
Linear Model" (although the former is a subset of the latter). See e.g. 
http://en.wikipedia.org/wiki/Generalized_linear_model#Confusion_with_general_linear_models

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of ye tian 
[tianye...@gmail.com]
Sent: Wednesday, June 18, 2014 12:46 PM
To: Freesurfer
Subject: [Freesurfer] GLM: What's the link?

Hello Freesurfers,

I can not tell what the link is from the Mathematical Background in mri_glmfit 
. Also, why is GLM performed instead of a linear regression (OLS or weighted LS 
)? I can not see how logistic, probit, etc is better.

Thank you very much!

Sincerely,
Ye

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Re: [Freesurfer] Command '-qa' in TRACULA

[Watson, Christopher]

Are you sure your path isn't look for the older "trac-all" first? If you didn't 
remove/overwrite it, that is.
Type "which trac-all" (without the quotes) and see if the correct one is shown.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anri WATANABE 
[z2aa...@koto.kpu-m.ac.jp]
Sent: Friday, December 12, 2014 1:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Command '-qa' in TRACULA

I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all 
-corr -c the_name_of_my_configuration_file, but it failed.
I pasted the log below and do you have any advices?

Thank you,
Anri



[watanabeanris-Mac-Pro:~] watanabeanri% trac-all -corr -c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial

INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons

INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c 
/volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/dmrirc.local -log 
/volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.log -cmd 
/volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc

#-


-I omitted a part of log in an image correction step-


Computing mean across frames

Writing to /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz

bet /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz 
/volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain.nii.gz -m -f 0.3

mv -f 
/volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain_mask.nii.gz 
/volumes/mybook/Anri/diffusion_tutorial/HC_002/dlabel/diff

#-

trac-preproc finished without error at Fri Dec 12 14:04:04 JST 2014

[watanabeanris-Mac-Pro:~] watanabeanri% trac-all -qa -c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial

ERROR: flag -qa unrecognized

-qa -c /volumes/mybook/Anri/diffusion_tutorial/dmrirc.tutorial

[watanabeanris-Mac-Pro:~] watanabeanri%


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2014-12-12 11:38 GMT+09:00 Anri WATANABE 
mailto:z2aa...@koto.kpu-m.ac.jp>>:
Thanks, Anastasia.
I'm worried about that a quality assessment step is not run because there are 
no presentation about "-qa" when I type "trac-all" in terminal (other steps are 
presented.)
Do you mean QA step will be run even if no mention about it?

Thanks in advance,
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2014-12-12 4:48 GMT+09:00 Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>>:

Hi Anri - This is not a command itself, it's an option of the trac-all command. 
So you need to run:
trac-all -qa -c the_name_of_your_configuration_file

Or, if you just run the entire preprocessing:
trac-all -prep -c the_name_of_your_configuration_file
then the motion QA measures will be computed by default as one of the many 
steps of the preprocessing.

You can run "trac-all" without any arguments to see usage information on all 
the the different options.

Hope this helps,
a.y


On Tue, 9 Dec 2014, Anri WATANABE wrote:

Thank you, Anastasia.
I had downloaded the updated software and unzipped it, but I couldn't find
the command "-qa."
I found "-qa" in the trac-all text file in the updated software.
However there are no "-qa" in terminal when I run "trac-all."
Do I have to move the file somewhere?

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2014-11-22 7:22 GMT+09:00 Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>>:

  Hi Anri - See here, and follow the link "software update":

  http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments

  The -qa option was added after 5.3 was released.

  a.y

  On Mon, 10 Nov 2014, Anri WATANABE wrote:

Dear FreeSurfer experts,

I'm running pre-processing steps in TRACULA
separatelly and could neither find the context about
quality

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Watson, Christopher]

I think certain filesystems don't support sym linking (e.g. FAT32). So that 
might be it.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme 
[katherine.da...@gmail.com]
Sent: Monday, December 15, 2014 5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula

After removing this I have a new (possibly unrelated error):
mv -f /media/Sokol/Subj/041/dmri/bvecs /media/Sokol/Subj/041/dmri/bvecs.norot
xfmrot /media/Sokol/Subj/041/dmri/dwi.ecclog 
/media/Sokol/Subj/041/dmri/bvecs.norot /media/Sokol/Subj/041/dmri/bvecs
ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz 
/media/Sokol/Subj/041/dmri/data.nii.gz
ln: creating symbolic link `/media/Sokol/Subj/041/dmri/data.nii.gz': Operation 
not permitted

This persists even when I run the command as the root user and regardless of 
the permissions settings of the folder and the fdwi.nii.gz file.

Any ideas?

On Mon, Dec 15, 2014 at 3:07 PM, Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:

It's hard to tell what's causing the error without seeing the entire 
trac-all.log. However, by glancing at your config file you seem to still have 
B0 inhomogeneity correction turned on (dob0 = 1) but without specifying any 
field map dicoms. I'd turn it off and see if that fixes it.


On Mon, 15 Dec 2014, Katherine Damme wrote:

Where would I be specifying a directory as an input/output?

I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c dmri.fy

On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
  Hi Katerine

  the COR-* format is an old one that we don't use anymore. If you specify 
a directory as an
  input/output we will assume that it contains COR files, which is probably 
what you are seeing.

  cheers
  Bruce


  On Sun, 14 Dec 2014, Katherine Damme wrote:

At what point is the COR-*.info file made?
I got the following error:

corRead(): can't open file /media/Sokol/Subj/COR-.info
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/Sokol/Subj/...
Linux 
kate.ad.wcas.northwestern.edu 
2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec
13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 12 12:54:40 CST 2014

[ksd770@kate 041]# ls /media/Sokol/Subj/COR-*

On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>> 
wrote:

  No, those are field maps used to correct for inhomogeneities 
in
  the main magnetic field (which in MRI lingo is referred to as
  the B0 field, not to be confused with the b=0 images). You can
  skip that correction (you have to skip it if you don't have
  field maps).

  On Thu, 11 Dec 2014, Katherine Damme wrote:

I am sorry, I am a bit confused. What am I supposed
to be specifying under
the b0mlist and b0plist?

I thought that it was the B0 low-b image from
diffusion.

Thank you!

On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki

mailto:ayend...@nmr.mgh.harvard.edu>> wrote:

  Hi Kate - The screenshot looks more like a
low-b image from a
  diffusion scan than a field map. In case this
helps, the phase
  map data will have either 2 volumes (2 phase
maps acquired at
  different echo times) or 1 volume (the
difference of 2 such
  phase maps).

  Best,
  a.y

  On Thu, 11 Dec 2014, Katherine Damme wrote:

Hello


Has anyone else had the problem of
tracula not
recognizing the format of the
phase map?

 I opened the B0 in fslview and it
appeared normal
(see screenshot). Any
help that you can offer would be greatly
appreciated! Thank you!

Thank you!

Kate Damme


On Fri, Nov 21, 2014 at 4:02 PM,
   

Re: [Freesurfer] Clarification on centos version/updates/patches

[Watson, Christopher]

Hi Nick,
So would you recommend I install Centos 6 on the new workstation?
In addition, I've run recon-all on a large study group (>100); I take it I'll 
have to re-run all of them?

Thanks,
Chris



Chris,

yes, the centos5 build freesurfer 5.1 will work on centos6 (we use it
in-house).  when the v5.2 release of freesurfer is ready (hopefully at
the end of may) you will want to use the centos6 build, as it will get a
bit better performance because of the compiler and some openmp options.

n.


On Wed, 2012-04-11 at 10:48 -0400, Chris Watson wrote:
> H i Nick,
> Will the centos5 build of v5.1 work with centos6? I'm getting a new 
> workstation and want to know which version of centos is better to install.
> 
> On 04/10/2012 10:08 AM, Nick Schmansky wrote:
> > Wil,
> >
> > Hi, the contents of that 'misc' directory is just a filedrop of sorts to
> > supply fixes to individuals who need particular updates.  We dont supply
> > formal patches, as it gets too unwieldy to track versions.  Rather bug
> > fixes are documented (mostly!) on the ReleaseNotes page with links to
> > fixes.
> >
> > We have a centos6 build, but dont release it.  We will for the next
> > release, v5.2, hopefully by the end of May, as the centos6 build runs a
> > little faster than the centos4/5 build because it uses a newer gcc, but
> > this will mean it wont be possible to mix versions, and a centos6 platform
> > (or kernel 2.6.32-220.7.1.el6.x86_6) will be needed.
> >
> > mri_info versioning wont affect the stream.  i dont think it has any bug
> > fixes outstanding.
> >
> > i think the trac-all script is the same, the versioning is different
> > because our 'dev' tree version was committed to our 'stable' branch, and
> > the two have different versions (but the file is the same).
> >
> > n.
> >
> >
> >
> >> Hi-
> >>
> >> It would appear the stable release for centos6 is ready for primetime
> >> 'stable5.1-bin.tgz'; Is this correct?  There is an updated version of
> >> 'mri_info' based on file size
> >> (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/).
> >>
> >>
> >> mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45
> >> mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32
> >>
> >> Which version is the most current?
> >>
> >> Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin
> >> to overwrite the extant files?
> >>
> >> Additionally, there is a versioning discrepancy between 'trac-all' located
> >> in
> >> (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/)
> >>
> >> '$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a
> >>
> >> and the version packaged with the cenos6_x86_65  'stable5.1-bin.tgz'
> >>
> >> '$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $'
> >>
> >> I did not comprehensively look for any other discrepancies-these just
> >> happened to stand out based on the work I was doing today.
> >>
> >> Thanks much,
> >> Wil
> >>
> >> ___
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> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom it is
> > addressed. If you believe this e-mail was sent to you in error and the 
> > e-mail
> > contains patient information, please contact the Partners Compliance 
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you in 
> > error
> > but does not contain patient information, please contact the sender and 
> > properly
> > dispose of the e-mail.
> >
> >
> 
> 


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[Freesurfer] mri_convert and image orientation; Analyze format

[Watson, Christopher]

Hello Freesurfers,
Lately I've been scratching my head about image orientation problems. What I do 
here is take the DICOM images and use mri_convert to convert them into SPM 
Analyze format. The command I use is:

mri_convert.x86_64.dev -dicomread2 "$experiment" --nskip ${nskip} \
"path/to/subj/dir/image" --out_type spm

So the output files we get are imageXXX.{hdr,img,mat}. So, I assume these truly 
are Analyze format and not NIfTI (if i'm incorrect please tell me, this would 
be very important). There are weird things SPM does concerning image 
orientation, so it's *very* important that I get this right (we do functional 
imaging on surgery candidates):

*Does mri_convert flip the images in any way?*

That is, if my DICOM images are in radiological convention, will the imageXXX 
images still be in radiological convention? I've been searching far and wide 
and have hit a wall. With patients, we can see the water pill on the right side 
of the forehead easily, but with the EPI functional images for our research 
subjects it's pretty much impossible to tell.

Thanks very much,
Chris Watson


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[Freesurfer] mri_convert: DICOM to nifti - multiple frames

[Watson, Christopher]

Hi, I'm interested in getting multiple nifti images for each time point, 
similar to this old thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03317.html

i.e., for a scan of 5 minutes and TR = 3, I would like 100 separate nifti 
images. This works fine when I set --out_type spm, but I'd like to start using 
the nifti format. The command I use:

mri_convert.x86_64.dev -dicomread2 i545236.MRDC.1 -ot nifti1 "$SUBJ_DIR/image"

only creates one file - image.nii. Is there a newer version of mri_convert that 
can do what I'm looking for? Here's the info:

$./mri_convert.x86_64.dev --all-info
ProgramName: mri_convert.x86_64.dev  ProgramArguments: --all-info  
ProgramVersion: $Name:  $  TimeStamp: 2008/09/25-14:47:29-GMT  BuildTimeStamp: 
Jun 15 2007 11:06:50  CVS: $Id: mri_convert.c,v 1.144 2007/06/14 03:18:56 greve 
Exp $  User: matlab7  Machine: occipital  Platform: Linux  PlatformVersion: 
2.6.9-55.0.6.ELsmp  CompilerName: GCC  CompilerVersion: 30300


Thanks,
Chris


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RE: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz

[Watson, Christopher]

The acquisitions are SPGRs, taken on either a GE 3T or 1.5T (I'm not exactly 
sure, I'm new to the job). Yea, in a lot of areas the dura is adjacent to the 
grey matter. Those are certainly the problem areas - in most other areas the 
segmentation is excellent. I'm not sure of the resolution.


-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 11/6/2007 8:49 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz
 
Hi Chris,

what type of acquisition are you using? Dura can be really hard to deal 
with, as it can look just like gm, depending on your MR parameters, and 
it is can also be physically adjacent to gm. That said, it's only usually a 
problem in localized areas. What resolution is your data? We have some 
newer sequences and code that avoid the dura, but they are by no means 
standard (and we only have them for Siemens).

cheers,
Bruce


On Tue, 6 Nov 2007, Chris Watson wrote:

> Hello all,
> I was wondering if there is a quick way to make edits to multiple slices of 
> the aseg.mgz (or the brainmask.mgz) volume.
>
> Specifically, I am working on my first subject, and it seems that on almost 
> every slice, pieces of the dura/skull/arachnoid/what-have-you get segmented 
> as cortex (less often, pieces of dura are included within the boundary of the 
> pial surface). I've worked on some slices by manually removing/de-segmenting 
> the pixels that need to go, but this is proving to be extraordinarily 
> time-consuming (some of the slices I've worked on can take 10 minutes easily; 
> perhaps I am obsessing too much, but am trying to get it as close to perfect 
> as it should look). For over 100 slices, even 5 minutes/slice of editing will 
> take several hours. I tried changing the mri_watershed parameter on another 
> subject, but that didn't seem to fix anything.
>
> Any tips to save me hours will be greatly appreciated.
>
> -Chris
> ___
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>
>
>



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[Freesurfer] recon-all error

[Watson, Christopher]

I was running a subject, and got this error:
recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010

make: *** 
[/usr/local/freesurfer/freesurfer-4.5.0/subjects/zhang_r/mri/aseg.mgz] Error 1

The disk is not full, and permissions are in order. I've run several other 
subjects with no problems. Initially my command line was "recon-all -autorecon2 
-s zhang_r"; then I tried again except with "-make autorecon2", and saw the 
same error.

It exits at SubCort Seg 
(mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z 
/usr/local/freesurfer/current/average/RB_all_2008-03-26.gca 
aseg.auto_noCCseg.mgz)

The last several lines of output are:
mri_ca_label GCA sequential renormalization: label 28 not consistently computed.

not using caudate to estimate GM means
setting label Right_VentralDC based on Left_VentralDC = 1.15 x +  0
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.01 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
Linux cwatson.homeunix.net 2.6.18-194.3.1.el5.centos.plus #1 SMP Wed May 19 
09:14:46 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux

Any ideas?
Chris
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Re: [Freesurfer] Red Hat vs. CentOs

[Watson, Christopher]

I've never had any problems with CentOS 4.x; I have had some with CentOS 5, but 
that was only when trying to run tksurfer, and that's really only because I 
didn't feel like playing around with it. I think it was an openGL issue, and 
not specifically a Freesurfer issue.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
dah...@nmr.mgh.harvard.edu [dah...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 10, 2010 2:21 PM
To: Don Hagler
Cc: freesurfer maillist; rai...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Red Hat vs. CentOs

Thanks Paul and Don. This leaves me a bit undecided. Any other experiences?
Dahlia.

>
> In my recent experience, no.  There were problems with entering text in
> tksurfer/tkmedit when running on the pre-installed RHEL that went away
> when CentOS was installed later.
>
>
>
>> Date: Mon, 9 Aug 2010 15:42:57 -0400
>> From: rai...@nmr.mgh.harvard.edu
>> To: dah...@nmr.mgh.harvard.edu
>> CC: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Red Hat vs. CentOs
>>
>>
>> Yes, it should be almost no different.
>>
>> On Mon, 9 Aug 2010 dah...@nmr.mgh.harvard.edu wrote:
>>
>> > Hi,
>> >
>> > I'd like to make sure that a Dell desktop with pre-installed RHEL
>> would
>> > work seamlessly with Freesurfer, equivalent to CentOS. Is this
>> correct?
>> >
>> > Thanks,
>> > Dahlia.
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >
>>
>> --
>> ---
>> Paul Rainesemail: raines at nmr.mgh.harvard.edu
>> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
>> 149 (2301) 13th Street Charlestown, MA 02129 USA
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>

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Re: [Freesurfer] running in the background?

[Watson, Christopher]

You can also just run e.g. "nohup recon-all -autorecon-all -s doe_j &"

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Scott Burns 
[sbu...@nmr.mgh.harvard.edu]
Sent: Tuesday, December 14, 2010 8:05 PM
To: Nathan Dankner
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] running in the background?

This tip comes from Sam at the helpdesk...

At the command prompt, type 'screen' and press enter.  This opens the terminal 
emulation program, aptly named screen.  In this new terminal, start your recon 
as you would normally, whether that's invoking a script of your making or 
typing in the standard 'recon -all '.  Once the job starts, either close 
the terminal window or press Ctrl-A followed by 'd'.  This detaches the screen 
session but safely keeps the  reconstruction pipeline going.

When you get back to your desk, type 'screen -r' at the command prompt to 
reattach to the screen session you created previously.  A new terminal will 
open and will contain all the output from the recon pipeline. Good luck.


Scott Burns
Kuperberg Lab
Martinos Center, MGH
sbu...@nmr.mgh.harvard.edu

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contains patient information, please contact the Partners Compliance HelpLine 
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error but does not contain patient information, please contact the sender and 
properly dispose of the e-mail.



On Tue, Dec 14, 2010 at 5:51 PM, Nathan Dankner 
mailto:nathan.dank...@vanderbilt.edu>> wrote:
Hi All,

I'm running freesurfer on a public station, so I need to sign out when I'm 
finished with sessions.  Has anyone found a suitable way to run freesurfer in 
the background?  I know that I can run matlab in the background here, so if 
there is a way to run the pipeline through matlab that may work... Thanks,

Nathan

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Re: [Freesurfer] running in the background?

[Watson, Christopher]

I should have clarified. I use nohup when I ssh into my workstation from 
elsewhere. I haven't tried it in which I would have to log out from the machine 
running recon-all.

From: Scott Burns [sbu...@nmr.mgh.harvard.edu]
Sent: Tuesday, December 14, 2010 9:54 PM
To: Watson, Christopher
Cc: Nathan Dankner; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] running in the background?

You can make it work with nohup? In the past I've had trouble and my thinking 
was that because recon-all starts many child processes, the  currently 
continues after the terminal is closed, but any subsequent process can't start. 
 That's why I've been using screen, but YMMV.


Scott Burns
Kuperberg Lab
Martinos Center, MGH
sbu...@nmr.mgh.harvard.edu<mailto:sbu...@nmr.mgh.harvard.edu>

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addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Partners Compliance HelpLine 
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error but does not contain patient information, please contact the sender and 
properly dispose of the e-mail.



On Tue, Dec 14, 2010 at 9:02 PM, Watson, Christopher 
mailto:christopher.wat...@childrens.harvard.edu>>
 wrote:
You can also just run e.g. "nohup recon-all -autorecon-all -s doe_j &"

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 On Behalf Of Scott Burns 
[sbu...@nmr.mgh.harvard.edu<mailto:sbu...@nmr.mgh.harvard.edu>]
Sent: Tuesday, December 14, 2010 8:05 PM
To: Nathan Dankner
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] running in the background?

This tip comes from Sam at the helpdesk...

At the command prompt, type 'screen' and press enter.  This opens the terminal 
emulation program, aptly named screen.  In this new terminal, start your recon 
as you would normally, whether that's invoking a script of your making or 
typing in the standard 'recon -all '.  Once the job starts, either close 
the terminal window or press Ctrl-A followed by 'd'.  This detaches the screen 
session but safely keeps the  reconstruction pipeline going.

When you get back to your desk, type 'screen -r' at the command prompt to 
reattach to the screen session you created previously.  A new terminal will 
open and will contain all the output from the recon pipeline. Good luck.


Scott Burns
Kuperberg Lab
Martinos Center, MGH
sbu...@nmr.mgh.harvard.edu<mailto:sbu...@nmr.mgh.harvard.edu><mailto:sbu...@nmr.mgh.harvard.edu<mailto:sbu...@nmr.mgh.harvard.edu>>

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.



On Tue, Dec 14, 2010 at 5:51 PM, Nathan Dankner 
mailto:nathan.dank...@vanderbilt.edu><mailto:nathan.dank...@vanderbilt.edu<mailto:nathan.dank...@vanderbilt.edu>>>
 wrote:
Hi All,

I'm running freesurfer on a public station, so I need to sign out when I'm 
finished with sessions.  Has anyone found a suitable way to run freesurfer in 
the background?  I know that I can run matlab in the background here, so if 
there is a way to run the pipeline through matlab that may work... Thanks,

Nathan

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