Re: [Freesurfer] T2pial shrinks pial surface

[Chris Adamson]

Thanks Bruce.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson
Sent: Monday, 7 March 2016 1:54 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

It is checkT2pial.zip

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, 7 March 2016 1:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Mon, 7 Mar
2016, Chris Adamson wrote:

> How can I upload it to you?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Monday, 7 March 2016 1:25 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>
> Hi Chris
>
> if you upload that dataset I'll try to take a look soon
>
> cheers
> Bruce
>
>
> On Mon, 7 Mar 2016, Chris Adamson wrote:
>
>>
>> The T2pial option mostly works beautifully. I have a few cases where 
>> the pial surface just shrinks globally and wraps over the white 
>> surface (see attached). I have checked the T2.mgz and the 
>> registration with the T1 is fine. This happens sometimes in one hemisphere 
>> only.
>>
>> Any ideas?
>>
>>  
>>
>> [IMAGE]
>>
>> Chris Adamson
>> Senior Research Officer
>> Developmental Imaging
>> Murdoch Childrens Research Institute
>> The Royal Children’s Hospital
>> Flemington Rd Parkville, Victoria 3052 AUS
>> T: (03) 9936 6780
>> E: chris.adam...@mcri.edu.au
>> www.mcri.edu.au
>>
>>  
>>
>> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]
>>
>>  
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Re: [Freesurfer] T2pial shrinks pial surface

[Chris Adamson]

It is checkT2pial.zip

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, 7 March 2016 1:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Mon, 7 Mar
2016, Chris Adamson wrote:

> How can I upload it to you?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Monday, 7 March 2016 1:25 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] T2pial shrinks pial surface
>
> Hi Chris
>
> if you upload that dataset I'll try to take a look soon
>
> cheers
> Bruce
>
>
> On Mon, 7 Mar 2016, Chris Adamson wrote:
>
>>
>> The T2pial option mostly works beautifully. I have a few cases where 
>> the pial surface just shrinks globally and wraps over the white 
>> surface (see attached). I have checked the T2.mgz and the 
>> registration with the T1 is fine. This happens sometimes in one hemisphere 
>> only.
>>
>> Any ideas?
>>
>>  
>>
>> [IMAGE]
>>
>> Chris Adamson
>> Senior Research Officer
>> Developmental Imaging
>> Murdoch Childrens Research Institute
>> The Royal Children’s Hospital
>> Flemington Rd Parkville, Victoria 3052 AUS
>> T: (03) 9936 6780
>> E: chris.adam...@mcri.edu.au
>> www.mcri.edu.au
>>
>>  
>>
>> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]
>>
>>  
>>
>> This e-mail and any attachments to it (the "Communication") are, 
>> unless otherwise stated, confidential, may contain copyright material 
>> and is for the use only of the intended recipient. If you receive the 
>> Communication in error, please notify the sender immediately by 
>> return e-mail, delete the Communication and the return e-mail, and do 
>> not read, copy, retransmit or otherwise deal with it. Any views 
>> expressed in the Communication are those of the individual sender 
>> only, unless expressly stated to be those of Murdoch Childrens 
>> Research Institute
>> (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does 
>> not accept liability in connection with the integrity of or errors in 
>> the Communication, computer virus, data corruption, interference or 
>> delay arising from or in respect of the Communication.
>>
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Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

[Joseph Dien]

never mind!  It turned out I was forgetting to run a script to move copies of 
the fixed fsgd files into their final locations.  Once I did so the files I 
posted worked fine.  Sorry for the false alarm and thanks for getting back to 
me!

Joe

> On Mar 3, 2016, at 12:18, Douglas N Greve  wrote:
> 
> I cannot replicate the error. What version of FS are you using? What 
> happens if you run
>  mri_glmfit --fsgd RPA-acc.fsgd
> or
> mri_glmfit --fsgd RPA-accGT.fsgd
> 
> 
> 
> On 02/29/2016 09:38 PM, Joseph Dien wrote:
>> Hi,
>>I’m having an fsgd error that has totally stumped me.  I’m trying to run 
>> the following command to compute the second level statistics:
>> 
>> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
>> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C 
>> normAcc.mtx
>> 
>> I get the error message:
>> 
>> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
>> gdfReadHeader: reading RPA-accGT.fsgd
>> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title
>> 
>> I used the utility flip to make sure the file was in UNIX format (with 
>> linefeeds).
>> I then double-checked by reading in the binary codes with Matlab’s fread and 
>> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).
>> 
>> Here is the contents of the fsgd file.
>> 
>> GroupDescriptorFile 1
>> Title RP1
>> Class Main
>> Variables LogoAcc NormAcc OrthAcc PhonAcc
>> InputRPA903  Main0.750.790.770.62
>> InputRPA906  Main0.810.810.830.74
>> InputRPA907  Main0.871   0.840.83
>> InputRPA908  Main0.910.930.950.89
>> InputRPA909  Main0.740.950.720.72
>> InputRPA910  Main0.850.960.810.79
>> InputRPA912  Main0.750.780.730.73
>> InputRPA914  Main0.7 0.850.830.81
>> InputRPA915  Main0.850.890.750.83
>> InputRPA916  Main0.840.920.870.72
>> InputRPA917  Main0.830.930.920.83
>> InputRPA918  Main0.870.910.790.85
>> InputRPA919  Main0.860.960.910.88
>> InputRPA920  Main0.840.920.870.84
>> InputRPA921  Main0.870.920.880.85
>> InputRPA922  Main0.8 0.9 0.9 0.72
>> 
>> What’s really driving me to distraction is that a previous version of this 
>> file (with a different set of participants) works fine.  I’m attaching both. 
>>  RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s 
>> fread, the first 85 characters (first four lines) of both files are 
>> identical.
>> 
>> I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.
>> 
>> Any help would be greatly appreciated!
>> 
>> Joe
>> 
>> 
>> 
>> 
>> 
>> Joseph Dien, PhD
>> Senior Research Scientist
>> Maryland Neuroimaging Center
>> University of Maryland, College Park
>> E-mail: jdie...@mac.com
>> Cell Phone: 202-297-8117
>> http://joedien.com
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
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> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 
> 
> 
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> 
> 
> 
> 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.



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com

Re: [Freesurfer] T2pial shrinks pial surface

[Bruce Fischl]

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Mon, 7 Mar 
2016, Chris Adamson wrote:



How can I upload it to you?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, 7 March 2016 1:25 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

Hi Chris

if you upload that dataset I'll try to take a look soon

cheers
Bruce


On Mon, 7 Mar 2016, Chris Adamson wrote:



The T2pial option mostly works beautifully. I have a few cases where
the pial surface just shrinks globally and wraps over the white
surface (see attached). I have checked the T2.mgz and the registration
with the T1 is fine. This happens sometimes in one hemisphere only.

Any ideas?

 

[IMAGE]

Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au

 

[IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]

 

This e-mail and any attachments to it (the "Communication") are,
unless otherwise stated, confidential, may contain copyright material
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read, copy, retransmit or otherwise deal with it. Any views expressed
in the Communication are those of the individual sender only, unless
expressly stated to be those of Murdoch Childrens Research Institute
(MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does
not accept liability in connection with the integrity of or errors in
the Communication, computer virus, data corruption, interference or
delay arising from or in respect of the Communication.

 

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Re: [Freesurfer] T2pial shrinks pial surface

[Chris Adamson]

How can I upload it to you?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, 7 March 2016 1:25 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

Hi Chris

if you upload that dataset I'll try to take a look soon

cheers
Bruce


On Mon, 7 Mar 2016, Chris Adamson wrote:

> 
> The T2pial option mostly works beautifully. I have a few cases where 
> the pial surface just shrinks globally and wraps over the white 
> surface (see attached). I have checked the T2.mgz and the registration 
> with the T1 is fine. This happens sometimes in one hemisphere only.
> 
> Any ideas?
> 
>  
> 
> [IMAGE]
> 
> Chris Adamson
> Senior Research Officer
> Developmental Imaging
> Murdoch Childrens Research Institute
> The Royal Children’s Hospital
> Flemington Rd Parkville, Victoria 3052 AUS
> T: (03) 9936 6780
> E: chris.adam...@mcri.edu.au
> www.mcri.edu.au
> 
>  
> 
> [IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]
> 
>  
> 
> This e-mail and any attachments to it (the "Communication") are, 
> unless otherwise stated, confidential, may contain copyright material 
> and is for the use only of the intended recipient. If you receive the 
> Communication in error, please notify the sender immediately by return 
> e-mail, delete the Communication and the return e-mail, and do not 
> read, copy, retransmit or otherwise deal with it. Any views expressed 
> in the Communication are those of the individual sender only, unless 
> expressly stated to be those of Murdoch Childrens Research Institute 
> (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does 
> not accept liability in connection with the integrity of or errors in 
> the Communication, computer virus, data corruption, interference or 
> delay arising from or in respect of the Communication.
> 
>  
> 
> P Please consider the environment before printing this email
> 
>  
> 
> 
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Re: [Freesurfer] T2pial shrinks pial surface

[Bruce Fischl]

Hi Chris

if you upload that dataset I'll try to take a look soon

cheers
Bruce


On Mon, 7 Mar 2016, Chris Adamson wrote:



The T2pial option mostly works beautifully. I have a few cases where the
pial surface just shrinks globally and wraps over the white surface (see
attached). I have checked the T2.mgz and the registration with the T1 is
fine. This happens sometimes in one hemisphere only.

Any ideas?

 

[IMAGE]

Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au

 

[IMAGE][IMAGE][IMAGE][IMAGE][IMAGE]

 

This e-mail and any attachments to it (the "Communication") are, unless
otherwise stated, confidential, may contain copyright material and is for
the use only of the intended recipient. If you receive the Communication in
error, please notify the sender immediately by return e-mail, delete the
Communication and the return e-mail, and do not read, copy, retransmit or
otherwise deal with it. Any views expressed in the Communication are those
of the individual sender only, unless expressly stated to be those of
Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its
related entities. MCRI does not accept liability in connection with the
integrity of or errors in the Communication, computer virus, data
corruption, interference or delay arising from or in respect of the
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Re: [Freesurfer] T2pial shrinks pial surface

[Chris Adamson]

5.3.0 stable

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
Sent: Monday, 7 March 2016 11:50 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2pial shrinks pial surface

What FreeSurfer version are you using?  Very small changes to the input images 
(e.g. a different random see for FreeSurfer) may be able to kick 
mris_make_surfaces out of that bug, though perhaps Bruce has fixed it.

Peace,

Matt.

From: 
>
 on behalf of Chris Adamson 
>
Reply-To: Freesurfer support list 
>
Date: Sunday, March 6, 2016 at 6:14 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
>
Subject: [Freesurfer] T2pial shrinks pial surface

The T2pial option mostly works beautifully. I have a few cases where the pial 
surface just shrinks globally and wraps over the white surface (see attached). 
I have checked the T2.mgz and the registration with the T1 is fine. This 
happens sometimes in one hemisphere only.
Any ideas?

[cid:image001.jpg@01D17868.5965F100]
Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au

[cid:image002.png@01D17868.5965F100][cid:image003.png@01D17868.5965F100][cid:image004.png@01D17868.5965F100][cid:image005.png@01D17868.5965F100][cid:image006.jpg@01D17868.5965F100]

This e-mail and any attachments to it (the "Communication") are, unless 
otherwise stated, confidential, may contain copyright material and is for the 
use only of the intended recipient. If you receive the Communication in error, 
please notify the sender immediately by return e-mail, delete the Communication 
and the return e-mail, and do not read, copy, retransmit or otherwise deal with 
it. Any views expressed in the Communication are those of the individual sender 
only, unless expressly stated to be those of Murdoch Childrens Research 
Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does 
not accept liability in connection with the integrity of or errors in the 
Communication, computer virus, data corruption, interference or delay arising 
from or in respect of the Communication.

PPlease consider the environment before printing this email


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Re: [Freesurfer] T2pial shrinks pial surface

[Matt Glasser]

What FreeSurfer version are you using?  Very small changes to the input
images (e.g. a different random see for FreeSurfer) may be able to kick
mris_make_surfaces out of that bug, though perhaps Bruce has fixed it.

Peace,

Matt.

From:   on behalf of Chris Adamson

Reply-To:  Freesurfer support list 
Date:  Sunday, March 6, 2016 at 6:14 PM
To:  "freesurfer@nmr.mgh.harvard.edu" 
Subject:  [Freesurfer] T2pial shrinks pial surface

The T2pial option mostly works beautifully. I have a few cases where the
pial surface just shrinks globally and wraps over the white surface (see
attached). I have checked the T2.mgz and the registration with the T1 is
fine. This happens sometimes in one hemisphere only.
Any ideas?
 
Chris Adamson
Senior Research Officer
Developmental Imaging
Murdoch Childrens Research Institute
The Royal Children¹s Hospital
Flemington Rd Parkville, Victoria 3052 AUS
T: (03) 9936 6780
E: chris.adam...@mcri.edu.au
www.mcri.edu.au 
 
 




 
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[Freesurfer] mris_anatomical_stats -th3

[Kaiming Yin]

Dear guys,

I checked one of my subjects file /stats/lh.aparc.stats, in which it said
the commandline as:

mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab subject1 lh white

what does the flag "-th3" mean? I'm using Freesurfer v6.0 beta.

Thanks,
Kaiming
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Re: [Freesurfer] mri_surf2surf dev vs stable

[marmaduke woodman]

On 03/06/2016 08:23 PM, marmaduke woodman wrote:

> mri_surf2surf ...--tval-xyz ./tvb/mri/T1.mgz

just to follow up, it seems --tval-xyz is a flag (no argument) on 
stable, but on dev takes an argument.

So, on stable, just

mri_surf2surf ... --tval-xyz

will run, but the resulting surface doesn't have the source subject's 
volume geometry info.

How can this be embedded in the surface to achieve the same effect as 
the --tval-xyz mri/T1.mgz flag in the dev version?


thanks,
Marmaduke
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[Freesurfer] mri_surf2surf dev vs stable

[marmaduke woodman]

Hi

The command

mri_surf2surf --srcsubject tvb --trgsubject fsaverage5 --hemi lh 
--sval-xyz pial --tval pial.tvb --tval-xyz ./tvb/mri/T1.mgz

works on dev (mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve), but on 
stable fails with

ERROR: Option ./tvb/mri/T1.mgz unknown


Is there a simple workaround or do I need to upgrade from stable to dev?


thanks,
Marmaduke
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Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

[Marie Schaer]

Hi all,

To follow-up on this issue if anyone else has the same problem, you need to 
modify one of the LGI functions as described in the release notes 
(http://freesurfer.net/fswiki/ReleaseNotes):

  *
LGI: issue when using Matlab 2013. the fix is to edit the file 
$FREESURFER_HOME/matlab/SearchProjectionOnPial.m and make these changes:


find this line:

< for t=1:step:size(perim,2)

and change to:

> si=max(size(perim));
> for t=1:step:si

Best,

Marie


On 05 Mar 2016, at 11:10, Marie Schaer 
> wrote:


Hi Ankita,

Did you get this error with only one subject, or with several different 
subjects? Have you checked your pial surface with freeview or tkmedit? No issue 
there? If your pial surfaces are fine and you get the issue for all the 
subjects you tried, send me a sample of pial surface + T1.mgz so that I can 
have a look.

Best,

Marie


On 05 Mar 2016, at 09:00, Ankita Chatterjee 
> wrote:

I ran the process, but it came up with an error that says "error: 
make_roi_paths did not complete successfully." I have attached the 
recon-all.log so hopefully someone can take a look at it and give me some 
pointers on what I can do to fix this.

Thank you again!

On Sat, Mar 5, 2016 at 8:35 AM, Ankita Chatterjee 
> wrote:
That's perfect. I think that solved the issue. It was not referencing the 
matlab files from freesurfer I guess. Thank you so much! It seems to be 
processing now!

Thanks!
Ankita

On Sat, Mar 5, 2016 at 8:05 AM, Ankita Chatterjee 
> wrote:
Thank you for the pointer Woo-Suk. So to do that, I just do an EXPORT PATH on 
Matlab? I am not very familiar with linux...

Thanks!
Ankita


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Re: [Freesurfer] Cortical thickness using freesurfer

[Bruce Fischl]

Hi Sahil

I believe with that command you are mapping the lh_cuneus.nii file to the 
surface of that subject, not fsaverage. Try visualizing it on the S01_LP 
inflated surface instead of fsaverage. If you want to map to fsaverage you 
can use surf2surf.


cheers
Bruce


On Fri, 4 Mar 2016, Sahil Bajaj wrote:


Dear all,

I am working on calculation of cortical thickness from a set of subjects. I
am following the instructionsfrom 
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness a
nd I am able to run up-to step-2 successfully i.e. I can display the ROIs on
fsaverage subject volume. But when I run step-3 using:

mri_vol2surf --mov /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii --reg
TT.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out ROI5.mgh
--reshape


It runs as follow:

(here lh_cuneus.nii is one of the ROIs,FTD_Data is my subject directory for
FreeSurfer and S01_LP is the output folder for one of the subjects after
running recon -all)


srcvol = /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii
srcreg = TT.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = 0.5
reshape = 1
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Reading surface /media/Storage/FTD_Data/fsaverage/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 1
using old
 2 0.1 0 1
using old
 3 0.2 0 1
using old
 4 0.3 0 1
using old
 5 0.4 0 1
using old
 6 0.5 0 1
using old
 7 0.6 0 1
using old
 8 0.7 0 1
using old
 9 0.8 0 1
using old
10 0.9 0 1
using old
Done mapping volume to surface
Number of source voxels hit = 75054
Reshaping 7 (nvertices = 163842)
Writing to ROI5.mgh
Dim: 23406 1 7


Although I don't see any error here but when I display using:

tksurfer fsaverage lh inflated -overlay ROI5.mgh -fthresh 0.5

it runs as follow:

setting fthresh to 0.5000
subject is fsaverage
hemi    is lh
surface is inflated
surfer: current subjects dir: /media/Storage/FTD_Data
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /media/Storage/FTD_Data/fsaverage/surf
checking for nofix files in 'inflated'
Reading image info (/media/Storage/FTD_Data/fsaverage)
Reading /media/Storage/FTD_Data/fsaverage/mri/orig.mgz
surfer: Reading header info from
/media/Storage/FTD_Data/fsaverage/mri/orig.mgz
surfer: vertices=163842, faces=327680
tkmedit: Trying to open ROI5.dat
surfer: Interpreting overlay volume ROI5.mgh as encoded scalar volume.
surfer: curvature read: min=-0.673989 max=0.540227
surfer: single buffered window
surfer: tkoInitWindow(fsaverage)
surfer: using interface
/home/sahil/Softwares/freesurfer/tktools/tksurfer.tcl
Reading /home/sahil/Softwares/freesurfer/tktools/tkm_common.tcl
Reading /home/sahil/Softwares/freesurfer/tktools/tkm_wrappers.tcl
Reading /home/sahil/Softwares/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/sahil/Softwares/freesurfer/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...


Again, I don't see any error here. But ROI ROI5.mgh is not displayed on the
fsaverage surface. I tried to overlay ROI5.mgh on lh inflated using freeview
as well but ROI5.mgh is nowhere.


I would really appreciate any help.


Thanks,

Sahil
--
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
Office: 713-363-9003
E-mail:sahil.ne...@gmail.com

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Re: [Freesurfer] mean thickness

[Bruce Fischl]

Hi Caroline

how  did you generate the Gnumeric file? And what operating 
system/hardware are you using? Also, please send us the recon-all.log for 
one of the subjects that you see this happening


cheers
Bruce

On Fri, 4 Mar 2016, 
Caroline Beelen wrote:




Dear Freesurfer team,

 

Forgive me if this is a foolish question…

 

I wanted to overlook cortical thickness, area and volume measures in
Gnumeric file after recon-all (checking edits made). However, for several
subjects I noticed that the values of mean thickness (final column) were
calculated wrong, whereas this is not the case for their independent
cortical thickness values. For instance, this happened to subject A09. I’m
including the excel file to show the example. In the gnumeric file the
number for this subject was depicted as 2/4964 instead of 2.4 etc.. What
could have went wrong?

 

Thank you for your answer in advance.

 

Kind regards, Caroline


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Re: [Freesurfer] Recon Reprocessing Issues

[Bruce Fischl]

Hi Champe

can you send us the recon-all.log file?

cheers
Bruce
On Sun, 6 Mar 2016, Champe Barton 
wrote:



Hi Freesurfer People,

I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I
have System Integrity Protection disabled (though I hadn’t experienced any
issues that could have been a result of that function). Everything in
FreeSurfer works fine for me—I ran recon-all and successfully processed
dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
the pial and white surfaces, and I successfully deleted unnecessary voxels
and added a set of control points (in both cases, being careful to make and
save the changes on all necessary slices with the brainmask volume
highlighted). My only issue is that when I reprocess the data using
recon-all -autorecon2-cp -autorecon3 -subjid , it runs
through the reconstruction without error and then shows no changes at all in
freeview when I view the volumes/surfaces. The deleted voxels still appear
deleted and I can still load the control points, so why wouldn’t it make the
changes?

And just to provide a little extra info: I encounter the same problem when I
reprocess the tutorial data for the pial edits tutorial. I delete the voxels
as instructed, save the file, reprocess it without error, and then nothing’s
changed when I view it all again in freeview.

Any help would be HUGELY appreciated—I’ve stressed over this for weeks
trying to get my computer to function properly so that I can begin my work
as a research assistant in a neuropsych lab editing and analyzing brain
scans with FreeSurfer.

Thanks,
Champe
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