date:20180221

[Freesurfer] Unsubscribe Mailing List

2018-02-21 Thread Duy Nguyen

Hi Freesurfer Team

Please unsubscribe my email from the list
Email: duynguyen@gmail.com

Thanks
-- 
Sent from Iphone
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Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

2018-02-21 Thread zuxfoucault Wong

Yes! I got better results now! Thanks!!

On Thu, Feb 22, 2018 at 12:57 AM Kirstie Whitaker  wrote:

> Hi Foucalt,
>
> I think you need to set the threshold to slightly larger than 0 otherwise
> you're taking the center of mass of the whole image (including the 0s) when
> really you want to exclude the 0s and only look at the individual regions.
>
> I changed --thmin 0  to --thmin 0.1 and the results looked good.
>
> Kx
>
> On 21 February 2018 at 09:28, zuxfoucault Wong 
> wrote:
>
>> Attach name file and result file.
>>
>> Thank you for your time!
>>
>> Best,
>> Foucault
>>
>> On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong 
>> wrote:
>>
>>> Hi Kirstie,
>>>
>>> Thank you very much for the suggestions!
>>> I modified my snippet to prevent it from looping the same value and
>>> still got the same results?
>>>
>>> ##
>>> input=($(cat ./names_68parc.txt))
>>> labels=()
>>> hemis=()
>>> j=0
>>> for i in "${input[@]}"; do
>>> if [[ $i == lh_* ]]; then
>>> hemis[j]="lh"
>>> i=$(echo $i | sed 's/^lh_//g')
>>> labels[j]="$i"
>>> (( j++ ))
>>> elif [[ $i == rh_* ]]; then
>>> hemis[j]="rh"
>>> i=$(echo $i | sed 's/^rh_//g')
>>> labels[j]="$i"
>>> (( j++ ))
>>> fi
>>> done
>>>
>>> nlabel=68
>>> if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then
>>> echo " number of label not match "
>>> fi
>>>
>>>
>>> for hemi in lh rh; do
>>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
>>> done
>>>
>>> for ((i=0;i<${#labels[@]};i++)); do
>>> mri_surfcluster --in
>>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness
>>> --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum
>>> ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi
>>> ${hemis[i]} --subject fsaverage
>>> tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/  */ /g' | cut
>>> -d' ' -f6-8 >> ./labels/68parc.centroids.txt
>>> done
>>> ##
>>>
>>>
>>> The output message of mri_surfcluster:
>>> ##
>>> thsign = abs, id = 0
>>> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman
>>> Exp $
>>> hemi   = rh
>>> srcid  =
>>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.thickness
>>> srcsubjid  = fsaverage
>>> srcsurf= white
>>> srcframe   = 0
>>> thsign = abs
>>> thmin  = 0
>>> thmax  = -1
>>> fdr= -1
>>> minarea= 0
>>> xfmfile= talairach.xfm
>>> clabelfile = ./labels/rh.lateraloccipital.label
>>> clabelinv  = 0
>>> nth = -1
>>> sumfile  = ./labels/sum.rh.lateraloccipital
>>> subjectsdir= /usr/local/freesurfer_orig/subjects
>>> FixMNI = 1
>>> Loading clabel ./labels/rh.lateraloccipital.label.
>>> Found 5963 points in clabel.
>>> - XFM matrix (RAS2RAS) ---
>>>
>>> /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm
>>>  1.0   0.0   0.0   0.0;
>>>  0.0   1.0   0.0   0.0;
>>>  0.0   0.0   1.0   0.0;
>>>  0.0   0.0   0.0   1.0;
>>> 
>>> Reading source surface
>>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.white
>>> Done reading source surface
>>> Computing metric properties
>>> Loading source values
>>> number of voxels in search space = 5963
>>> Done loading source values (nvtxs = 163842)
>>> overall max = 3.19752 at vertex 122846
>>> overall min = 0 at vertex 0
>>> surface nvertices 163842
>>> metric props tot surface area 65020.839844
>>> group_avg_vtxarea_loaded 1
>>> masked surface area 4459.747559
>>> NOT Adjusting threshold for 1-tailed test
>>> thminadj = 0
>>> Searching for Clusters ...
>>> thmin=0.00 (0.00), thmax=-1.00 (-1), thsignid=0,
>>> minarea=0.00
>>> Found 1 clusters
>>> Max cluster size 82167.00
>>> INFO: fixing MNI talairach coordinates
>>>
>>>
>>> On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker 
>>> wrote:
>>>
 Hi Foucault,

 In the snippet you added you don’t define the labels variable (which
 you subsequently loop over in for label in ${labels}).

 There are two possible mistakes that are easy to fix. One may be that
 you forgot to read in the labels! And the other is that to get all the
 values in an array you need ${labels[@]}.

 I don’t think you need greater precision than you have. The regions are
 pretty far apart in mm terms :)

 Kirstie

 Sent from my iPhone, please excuse any typos or excessive brevity

 On 21 Feb 2018, at 03:44, zuxfoucault Wong 
 wrote:

 Dear Freesurfer experts,

 Based on this
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/07.html
  , I
 wrote a short script to extract the centroids from Desikan-Killiany
 atlas.

 ##
 for hemi in lh rh; do

Re: [Freesurfer] Search angle limitation in the flirt registration

2018-02-21 Thread Douglas N Greve

you should post your question to the FSL list (they developed and 
support flirt)


On 02/21/2018 05:34 PM, Yixin Ma wrote:
> Hi freesurfer developers and users,
>
> I'm writing to ask about the search angle limitation (--searchrx, -- 
> searchry and --searchrz) in the flirt function. I use the search angle 
> option a lot for limited angle search, which usually generate a better 
> registration result compared with the broad angle search. But I still 
> don't quite understand how rx,ry and rz are defined and how negative 
> and positive angles affect the result. Because sometimes I find the 
> result after the angle limitation does not align well with my 
> expectation of rotation angle.
>
> Thank you for your help,
>
> Yixin Ma
>
> Brain Image and Analysis Center
>
> Duke university
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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[Freesurfer] Search angle limitation in the flirt registration

2018-02-21 Thread Yixin Ma

Hi freesurfer developers and users,

I'm writing to ask about the search angle limitation (--searchrx, --
searchry and --searchrz) in the flirt function. I use the search angle
option a lot for limited angle search, which usually generate a better
registration result compared with the broad angle search. But I still don't
quite understand how rx,ry and rz are defined and how negative and positive
angles affect the result. Because sometimes I find the result after the
angle limitation does not align well with my expectation of rotation angle.

Thank you for your help,

Yixin Ma

Brain Image and Analysis Center

Duke university
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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
dispose of the e-mail.

[Freesurfer] Extraction of cortical thickness in native space

2018-02-21 Thread Albrecht, Daniel S.

Hello,


We are attempting to extract cortical thickness values from a pre-defined ROI 
in MNI space.


Originally, we had followed the instructions detailed here:

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

for extraction in MNI space, but now wanted to extract thickness from 
individual subject T1 images in native space.


We attempted to use the same pipeline (e.g. register native space T1 to 
fsaverage) but were unable to get a good registration with several different 
tools.


Is there a better way to do this, either by improving the registration to 
fsaverage, or by transforming the ROI to native space (which we have done) and 
projecting that to a surface/label?


Any suggestions are welcome, and we appreciate the help!


Cheers,


Dan

VolumeRoiCorticalThickness - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Cortical Thickness of a Volume-defined ROI. This page describes the workflow to 
extract freesurfer cortical thickness values for a region-of-interest (ROI) 
defined in ...



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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Surface Errors

2018-02-21 Thread Douglas N Greve

yes, filedrop should be find

thanks


On 02/21/2018 04:44 PM, Emily Schwartz wrote:
> Hi Doug,
>
> I definitely can. I cannot use FTP from this computer for some reason. Can I 
> upload it via filedrop and should I send it to your email?
>
> Thanks,
>
> Emily
>
>
> 
> 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: Wednesday, February 21, 2018 4:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> I'm a little surprised you are getting them so frequently. Can you
> upload a couple of subjects so I can take a look?
>
>
>
> On 02/21/2018 02:52 PM, Emily Schwartz wrote:
>> Hi Doug,
>>
>> I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors 
>> so often?
>>
>> Best,
>>
>> Emily
>> 
>> 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: Wednesday, February 21, 2018 2:18 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> btw, what verions of FS are you using?
>>
>>
>> On 02/21/2018 01:25 PM, Emily Schwartz wrote:
>>> Got it, thank you so much!
>>>
>>> Best,
>>>
>>> Emily
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Wednesday, February 21, 2018 10:23 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> Hi Emily
>>>
>>> it is a segmentation error, but it's a pretty small one. It will mess up
>>> the thickness in a region a few mm^2. You could fix it by editing the
>>> wm.mgz if you really care about that spot
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 21 Feb 2018, Emily Schwartz wrote:
>>>
 Hi Doug,

 Thank you for getting back to me. I've attached two images (Slice165 and 
 Slice166) with an arrow pointing to the location. I am new at this, so 
 maybe I am wrong and it is not a segmentation error.

 I've also attached an additional image (Slice185) of what I think is a 
 type of topological error that I often see multiple times in a subject. Is 
 this a topological defect? If so, if it is only over 3 slices does it need 
 to be corrected?

 Thanks again,

 Emily
 
 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, February 20, 2018 4:59 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Surface Errors

 sorry, what kind of errors? I could not really tell from the images what
 the problem was


 On 02/20/2018 10:22 AM, Emily Schwartz wrote:
> Hi FreeSurfer community,
>
> I am working on elderly subjects and have had this kind of surface error 
> quite often in different locations. Usually, it's over about 3-4 slices 
> (in one view) and can be fixed, but I am finding multiple in almost every 
> subject and therefore taking a lot of time to edit (and then once 
> reprocessed new ones sometimes come up in different locations). I was 
> wondering if these are normal to have, minor surface errors that do not 
> necessarily need to be fixed. I have added images of an example below. 
> Here are some of the values I get from aparc.stats for caudal middle 
> frontal lh after manually editing:
>
> Surface area:
> Original - 2500 mm^2
> Edited -  2532 mm^2
>
> Grey volume:
> Original -  1710 mm^3
> Edited -  1727 mm^3
>
> Thickness avg
> Original -  4455 mm  std: 2.371
> Edited -  4445 mm  std: 2.365
>
> Although the thickness values only differ by 10 mm, we are a little 
> concerned because the difference is not within the standard deviation.
>
> Please let me know if all of these errors should be edited or if it may 
> be okay to keep the smaller segmentation/topological errors as they are.
>
> Thank you,
>
> Emily
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

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

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Emily Schwartz

Hi Doug,

I definitely can. I cannot use FTP from this computer for some reason. Can I 
upload it via filedrop and should I send it to your email?

Thanks,

Emily 



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: Wednesday, February 21, 2018 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface Errors

I'm a little surprised you are getting them so frequently. Can you
upload a couple of subjects so I can take a look?



On 02/21/2018 02:52 PM, Emily Schwartz wrote:
> Hi Doug,
>
> I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so 
> often?
>
> Best,
>
> Emily
> 
> 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: Wednesday, February 21, 2018 2:18 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> btw, what verions of FS are you using?
>
>
> On 02/21/2018 01:25 PM, Emily Schwartz wrote:
>> Got it, thank you so much!
>>
>> Best,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, February 21, 2018 10:23 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> Hi Emily
>>
>> it is a segmentation error, but it's a pretty small one. It will mess up
>> the thickness in a region a few mm^2. You could fix it by editing the
>> wm.mgz if you really care about that spot
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 21 Feb 2018, Emily Schwartz wrote:
>>
>>> Hi Doug,
>>>
>>> Thank you for getting back to me. I've attached two images (Slice165 and 
>>> Slice166) with an arrow pointing to the location. I am new at this, so 
>>> maybe I am wrong and it is not a segmentation error.
>>>
>>> I've also attached an additional image (Slice185) of what I think is a type 
>>> of topological error that I often see multiple times in a subject. Is this 
>>> a topological defect? If so, if it is only over 3 slices does it need to be 
>>> corrected?
>>>
>>> Thanks again,
>>>
>>> Emily
>>> 
>>> 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, February 20, 2018 4:59 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> sorry, what kind of errors? I could not really tell from the images what
>>> the problem was
>>>
>>>
>>> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
 Hi FreeSurfer community,

 I am working on elderly subjects and have had this kind of surface error 
 quite often in different locations. Usually, it's over about 3-4 slices 
 (in one view) and can be fixed, but I am finding multiple in almost every 
 subject and therefore taking a lot of time to edit (and then once 
 reprocessed new ones sometimes come up in different locations). I was 
 wondering if these are normal to have, minor surface errors that do not 
 necessarily need to be fixed. I have added images of an example below. 
 Here are some of the values I get from aparc.stats for caudal middle 
 frontal lh after manually editing:

 Surface area:
 Original - 2500 mm^2
 Edited -  2532 mm^2

 Grey volume:
 Original -  1710 mm^3
 Edited -  1727 mm^3

 Thickness avg
 Original -  4455 mm  std: 2.371
 Edited -  4445 mm  std: 2.365

 Although the thickness values only differ by 10 mm, we are a little 
 concerned because the difference is not within the standard deviation.

 Please let me know if all of these errors should be edited or if it may be 
 okay to keep the smaller segmentation/topological errors as they are.

 Thank you,

 Emily




 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Douglas N Greve

I'm a little surprised you are getting them so frequently. Can you 
upload a couple of subjects so I can take a look?



On 02/21/2018 02:52 PM, Emily Schwartz wrote:
> Hi Doug,
>
> I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so 
> often?
>
> Best,
>
> Emily
> 
> 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: Wednesday, February 21, 2018 2:18 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> btw, what verions of FS are you using?
>
>
> On 02/21/2018 01:25 PM, Emily Schwartz wrote:
>> Got it, thank you so much!
>>
>> Best,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, February 21, 2018 10:23 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> Hi Emily
>>
>> it is a segmentation error, but it's a pretty small one. It will mess up
>> the thickness in a region a few mm^2. You could fix it by editing the
>> wm.mgz if you really care about that spot
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 21 Feb 2018, Emily Schwartz wrote:
>>
>>> Hi Doug,
>>>
>>> Thank you for getting back to me. I've attached two images (Slice165 and 
>>> Slice166) with an arrow pointing to the location. I am new at this, so 
>>> maybe I am wrong and it is not a segmentation error.
>>>
>>> I've also attached an additional image (Slice185) of what I think is a type 
>>> of topological error that I often see multiple times in a subject. Is this 
>>> a topological defect? If so, if it is only over 3 slices does it need to be 
>>> corrected?
>>>
>>> Thanks again,
>>>
>>> Emily
>>> 
>>> 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, February 20, 2018 4:59 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Surface Errors
>>>
>>> sorry, what kind of errors? I could not really tell from the images what
>>> the problem was
>>>
>>>
>>> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
 Hi FreeSurfer community,

 I am working on elderly subjects and have had this kind of surface error 
 quite often in different locations. Usually, it's over about 3-4 slices 
 (in one view) and can be fixed, but I am finding multiple in almost every 
 subject and therefore taking a lot of time to edit (and then once 
 reprocessed new ones sometimes come up in different locations). I was 
 wondering if these are normal to have, minor surface errors that do not 
 necessarily need to be fixed. I have added images of an example below. 
 Here are some of the values I get from aparc.stats for caudal middle 
 frontal lh after manually editing:

 Surface area:
 Original - 2500 mm^2
 Edited -  2532 mm^2

 Grey volume:
 Original -  1710 mm^3
 Edited -  1727 mm^3

 Thickness avg
 Original -  4455 mm  std: 2.371
 Edited -  4445 mm  std: 2.365

 Although the thickness values only differ by 10 mm, we are a little 
 concerned because the difference is not within the standard deviation.

 Please let me know if all of these errors should be edited or if it may be 
 okay to keep the smaller segmentation/topological errors as they are.

 Thank you,

 Emily




 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>> ___
>> Freesurfer mailing list
>>

Re: [Freesurfer] Lookup Table

2018-02-21 Thread Diamond, Bram Ryder

Hi Jason,


You can use mri_binarize to extract a wm-hypointensities.mgz volume and view 
that over the orig.mgz.  The following will make a binary volume called 
wm-hypointensities.mgz from all voxels in the aseg.mgz with an intensity of 77 
- all voxels labeled wm-hypointensities:


mri_binarize --i mri/aseg.mgz --o mri/wm-hypointensities.mgz --match 77


Then view the new wm-hypointensities volume over the orig.mgz like this:


freeview mri/orig.mgz mri/wm-hypointensities.mgz:colormap=heat


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ledesma, Jason 

Sent: Wednesday, February 21, 2018 1:53:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Lookup Table


Hi,


When viewing MRI mgz images in Freeview, is it possible to only look at certain 
structures specified in the look up table?  That is, to only view colorization 
of one structure to view it more concisely?  Specifically, we want to look at 
wm-hypointensities to see lesion approximations. Thanks.


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



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Re: [Freesurfer] Surface Errors

2018-02-21 Thread Emily Schwartz

Got it, thank you so much!

Best,

Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 21, 2018 10:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Surface Errors

Hi Emily

it is a segmentation error, but it's a pretty small one. It will mess up
the thickness in a region a few mm^2. You could fix it by editing the
wm.mgz if you really care about that spot

cheers
Bruce


On Wed, 21 Feb 2018, Emily Schwartz wrote:

> Hi Doug,
>
> Thank you for getting back to me. I've attached two images (Slice165 and 
> Slice166) with an arrow pointing to the location. I am new at this, so maybe 
> I am wrong and it is not a segmentation error.
>
> I've also attached an additional image (Slice185) of what I think is a type 
> of topological error that I often see multiple times in a subject. Is this a 
> topological defect? If so, if it is only over 3 slices does it need to be 
> corrected?
>
> Thanks again,
>
> Emily
> 
> 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, February 20, 2018 4:59 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> sorry, what kind of errors? I could not really tell from the images what
> the problem was
>
>
> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
>> Hi FreeSurfer community,
>>
>> I am working on elderly subjects and have had this kind of surface error 
>> quite often in different locations. Usually, it's over about 3-4 slices (in 
>> one view) and can be fixed, but I am finding multiple in almost every 
>> subject and therefore taking a lot of time to edit (and then once 
>> reprocessed new ones sometimes come up in different locations). I was 
>> wondering if these are normal to have, minor surface errors that do not 
>> necessarily need to be fixed. I have added images of an example below. Here 
>> are some of the values I get from aparc.stats for caudal middle frontal lh 
>> after manually editing:
>>
>> Surface area:
>> Original - 2500 mm^2
>> Edited -  2532 mm^2
>>
>> Grey volume:
>> Original -  1710 mm^3
>> Edited -  1727 mm^3
>>
>> Thickness avg
>> Original -  4455 mm  std: 2.371
>> Edited -  4445 mm  std: 2.365
>>
>> Although the thickness values only differ by 10 mm, we are a little 
>> concerned because the difference is not within the standard deviation.
>>
>> Please let me know if all of these errors should be edited or if it may be 
>> okay to keep the smaller segmentation/topological errors as they are.
>>
>> Thank you,
>>
>> Emily
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error 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] Surface Errors

2018-02-21 Thread Emily Schwartz

Hi Doug,

I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so 
often? 

Best,

Emily

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: Wednesday, February 21, 2018 2:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface Errors

btw, what verions of FS are you using?


On 02/21/2018 01:25 PM, Emily Schwartz wrote:
> Got it, thank you so much!
>
> Best,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 21, 2018 10:23 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Surface Errors
>
> Hi Emily
>
> it is a segmentation error, but it's a pretty small one. It will mess up
> the thickness in a region a few mm^2. You could fix it by editing the
> wm.mgz if you really care about that spot
>
> cheers
> Bruce
>
>
> On Wed, 21 Feb 2018, Emily Schwartz wrote:
>
>> Hi Doug,
>>
>> Thank you for getting back to me. I've attached two images (Slice165 and 
>> Slice166) with an arrow pointing to the location. I am new at this, so maybe 
>> I am wrong and it is not a segmentation error.
>>
>> I've also attached an additional image (Slice185) of what I think is a type 
>> of topological error that I often see multiple times in a subject. Is this a 
>> topological defect? If so, if it is only over 3 slices does it need to be 
>> corrected?
>>
>> Thanks again,
>>
>> Emily
>> 
>> 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, February 20, 2018 4:59 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> sorry, what kind of errors? I could not really tell from the images what
>> the problem was
>>
>>
>> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
>>> Hi FreeSurfer community,
>>>
>>> I am working on elderly subjects and have had this kind of surface error 
>>> quite often in different locations. Usually, it's over about 3-4 slices (in 
>>> one view) and can be fixed, but I am finding multiple in almost every 
>>> subject and therefore taking a lot of time to edit (and then once 
>>> reprocessed new ones sometimes come up in different locations). I was 
>>> wondering if these are normal to have, minor surface errors that do not 
>>> necessarily need to be fixed. I have added images of an example below. Here 
>>> are some of the values I get from aparc.stats for caudal middle frontal lh 
>>> after manually editing:
>>>
>>> Surface area:
>>> Original - 2500 mm^2
>>> Edited -  2532 mm^2
>>>
>>> Grey volume:
>>> Original -  1710 mm^3
>>> Edited -  1727 mm^3
>>>
>>> Thickness avg
>>> Original -  4455 mm  std: 2.371
>>> Edited -  4445 mm  std: 2.365
>>>
>>> Although the thickness values only differ by 10 mm, we are a little 
>>> concerned because the difference is not within the standard deviation.
>>>
>>> Please let me know if all of these errors should be edited or if it may be 
>>> okay to keep the smaller segmentation/topological errors as they are.
>>>
>>> Thank you,
>>>
>>> Emily
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center

Re: [Freesurfer] Surface Errors

2018-02-21 Thread Douglas N Greve

btw, what verions of FS are you using?


On 02/21/2018 01:25 PM, Emily Schwartz wrote:
> Got it, thank you so much!
>
> Best,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 21, 2018 10:23 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Surface Errors
>
> Hi Emily
>
> it is a segmentation error, but it's a pretty small one. It will mess up
> the thickness in a region a few mm^2. You could fix it by editing the
> wm.mgz if you really care about that spot
>
> cheers
> Bruce
>
>
> On Wed, 21 Feb 2018, Emily Schwartz wrote:
>
>> Hi Doug,
>>
>> Thank you for getting back to me. I've attached two images (Slice165 and 
>> Slice166) with an arrow pointing to the location. I am new at this, so maybe 
>> I am wrong and it is not a segmentation error.
>>
>> I've also attached an additional image (Slice185) of what I think is a type 
>> of topological error that I often see multiple times in a subject. Is this a 
>> topological defect? If so, if it is only over 3 slices does it need to be 
>> corrected?
>>
>> Thanks again,
>>
>> Emily
>> 
>> 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, February 20, 2018 4:59 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Surface Errors
>>
>> sorry, what kind of errors? I could not really tell from the images what
>> the problem was
>>
>>
>> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
>>> Hi FreeSurfer community,
>>>
>>> I am working on elderly subjects and have had this kind of surface error 
>>> quite often in different locations. Usually, it's over about 3-4 slices (in 
>>> one view) and can be fixed, but I am finding multiple in almost every 
>>> subject and therefore taking a lot of time to edit (and then once 
>>> reprocessed new ones sometimes come up in different locations). I was 
>>> wondering if these are normal to have, minor surface errors that do not 
>>> necessarily need to be fixed. I have added images of an example below. Here 
>>> are some of the values I get from aparc.stats for caudal middle frontal lh 
>>> after manually editing:
>>>
>>> Surface area:
>>> Original - 2500 mm^2
>>> Edited -  2532 mm^2
>>>
>>> Grey volume:
>>> Original -  1710 mm^3
>>> Edited -  1727 mm^3
>>>
>>> Thickness avg
>>> Original -  4455 mm  std: 2.371
>>> Edited -  4445 mm  std: 2.365
>>>
>>> Although the thickness values only differ by 10 mm, we are a little 
>>> concerned because the difference is not within the standard deviation.
>>>
>>> Please let me know if all of these errors should be edited or if it may be 
>>> okay to keep the smaller segmentation/topological errors as they are.
>>>
>>> Thank you,
>>>
>>> Emily
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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[Freesurfer] Lookup Table

2018-02-21 Thread Ledesma, Jason

Hi,


When viewing MRI mgz images in Freeview, is it possible to only look at certain 
structures specified in the look up table?  That is, to only view colorization 
of one structure to view it more concisely?  Specifically, we want to look at 
wm-hypointensities to see lesion approximations. Thanks.


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



LA BioMed Warning: This email (and any attachments) is intended for the use of 
the person to which it is addressed. It may contain information that is 
privileged and confidential. As the recipient, you are obligated to maintain it 
in a safe, secure and confidential manner. Unauthorized disclosure or failure 
to maintain confidentiality may subject you to governmental penalties. Should 
you not be the intended recipient, please notify us by return email, and delete 
this message from your computer at once.

___
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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] Problem with cortical parcellation of rh but not lh

2018-02-21 Thread Bruce Fischl

Hi Amal

we need the entire directory tree for that subject
cheers
Bruce
On Wed, 21 Feb 2018, Amal 
Achaibou wrote:

Hi,

Yes I've seen it for multiple subjects.

I'm using version 6.

Here are the results for one participants, let me know if you need any other 
file.

Thanks

Amal

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Thursday, February 15, 2018 8:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh  
Hi Amal

this happens for multiple subjects? What version are you using? I have
only ever seen this very rarely and usually for an atypical (e.g.
multiple central sulci) folding pattern. Can you upload a subject so I
can take a look?

cheers
Bruce
On Tue, 13 Feb 2018, Amal Achaibou wrote:

>
> Hello,
>
> I'm new to freesurfer and have been trying to use it for cortical 
parcellation of individual T1s
> running recon-all -s subID -i sunT1 -all command. I'm specifically interested 
in getting
> parahippocampal and perirhinal ROIs for each individual. It appears that the 
parcellation is
correct
> for the left hemisphere but not for the right hemisphere... I found that 
there were also
mislabeling
> for precentral and postcentral gyrus (as easy gyri to identify), and that 
regardless of if I
looked
> at the aparc.annot or the aparc.DKTatlas.annot parcellation scheme.
>
> Is there any reason why I have this systematic mistake? Attached is the 
example for one subject
> (others looked very similar).
>
>
> Thanks
>
>
> Amal
>
>
>___
_
>
>
>
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Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

2018-02-21 Thread Kirstie Whitaker

Hi Foucalt,

I think you need to set the threshold to slightly larger than 0 otherwise
you're taking the center of mass of the whole image (including the 0s) when
really you want to exclude the 0s and only look at the individual regions.

I changed --thmin 0  to --thmin 0.1 and the results looked good.

Kx

On 21 February 2018 at 09:28, zuxfoucault Wong 
wrote:

> Attach name file and result file.
>
> Thank you for your time!
>
> Best,
> Foucault
>
> On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong 
> wrote:
>
>> Hi Kirstie,
>>
>> Thank you very much for the suggestions!
>> I modified my snippet to prevent it from looping the same value and still
>> got the same results?
>>
>> ##
>> input=($(cat ./names_68parc.txt))
>> labels=()
>> hemis=()
>> j=0
>> for i in "${input[@]}"; do
>> if [[ $i == lh_* ]]; then
>> hemis[j]="lh"
>> i=$(echo $i | sed 's/^lh_//g')
>> labels[j]="$i"
>> (( j++ ))
>> elif [[ $i == rh_* ]]; then
>> hemis[j]="rh"
>> i=$(echo $i | sed 's/^rh_//g')
>> labels[j]="$i"
>> (( j++ ))
>> fi
>> done
>>
>> nlabel=68
>> if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then
>> echo " number of label not match "
>> fi
>>
>>
>> for hemi in lh rh; do
>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
>> done
>>
>> for ((i=0;i<${#labels[@]};i++)); do
>> mri_surfcluster --in /usr/local/freesurfer_orig/sub
>> jects/fsaverage/surf/${hemis[i]}.thickness --clabel
>> ./labels/${hemis[i]}.${labels[i]}.label --sum
>> ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi
>> ${hemis[i]} --subject fsaverage
>> tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/  */ /g' | cut
>> -d' ' -f6-8 >> ./labels/68parc.centroids.txt
>> done
>> ##
>>
>>
>> The output message of mri_surfcluster:
>> ##
>> thsign = abs, id = 0
>> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman
>> Exp $
>> hemi   = rh
>> srcid  = /usr/local/freesurfer_orig/sub
>> jects/fsaverage/surf/rh.thickness
>> srcsubjid  = fsaverage
>> srcsurf= white
>> srcframe   = 0
>> thsign = abs
>> thmin  = 0
>> thmax  = -1
>> fdr= -1
>> minarea= 0
>> xfmfile= talairach.xfm
>> clabelfile = ./labels/rh.lateraloccipital.label
>> clabelinv  = 0
>> nth = -1
>> sumfile  = ./labels/sum.rh.lateraloccipital
>> subjectsdir= /usr/local/freesurfer_orig/subjects
>> FixMNI = 1
>> Loading clabel ./labels/rh.lateraloccipital.label.
>> Found 5963 points in clabel.
>> - XFM matrix (RAS2RAS) ---
>> /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms
>> /talairach.xfm
>>  1.0   0.0   0.0   0.0;
>>  0.0   1.0   0.0   0.0;
>>  0.0   0.0   1.0   0.0;
>>  0.0   0.0   0.0   1.0;
>> 
>> Reading source surface /usr/local/freesurfer_orig/sub
>> jects/fsaverage/surf/rh.white
>> Done reading source surface
>> Computing metric properties
>> Loading source values
>> number of voxels in search space = 5963
>> Done loading source values (nvtxs = 163842)
>> overall max = 3.19752 at vertex 122846
>> overall min = 0 at vertex 0
>> surface nvertices 163842
>> metric props tot surface area 65020.839844
>> group_avg_vtxarea_loaded 1
>> masked surface area 4459.747559
>> NOT Adjusting threshold for 1-tailed test
>> thminadj = 0
>> Searching for Clusters ...
>> thmin=0.00 (0.00), thmax=-1.00 (-1), thsignid=0,
>> minarea=0.00
>> Found 1 clusters
>> Max cluster size 82167.00
>> INFO: fixing MNI talairach coordinates
>>
>>
>> On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker 
>> wrote:
>>
>>> Hi Foucault,
>>>
>>> In the snippet you added you don’t define the labels variable (which you
>>> subsequently loop over in for label in ${labels}).
>>>
>>> There are two possible mistakes that are easy to fix. One may be that
>>> you forgot to read in the labels! And the other is that to get all the
>>> values in an array you need ${labels[@]}.
>>>
>>> I don’t think you need greater precision than you have. The regions are
>>> pretty far apart in mm terms :)
>>>
>>> Kirstie
>>>
>>> Sent from my iPhone, please excuse any typos or excessive brevity
>>>
>>> On 21 Feb 2018, at 03:44, zuxfoucault Wong 
>>> wrote:
>>>
>>> Dear Freesurfer experts,
>>>
>>> Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
>>> 2013-September/07.html , I wrote a short script to extract the
>>> centroids from Desikan-Killiany atlas.
>>>
>>> ##
>>> for hemi in lh rh; do
>>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
>>> for label in ${labels}; do
>>> mri_surfcluster --in /usr/local/freesurfer/subjects
>>> /fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label
>>> --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi}

[Freesurfer] local gyrification index - contrast and doss vs. dods

2018-02-21 Thread C.P.E. Rollins

Dear Freesurfer Developers,

I'm following the very well-documented steps proposed by Marie Schaer 
for measuring local gyrification index in the paper "How to Measure 
Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute 
Local Gyrification Index" 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). I have 2 
questions I was wondering whether you might be able to answer:

1) Based on the contrast and FSDG files described in the paper (patients 
vs. controls, controlling for age and gender), would significant regions 
in blue refer to regions with reduced gyrification in patients relative 
to controls (patient LGI < control LGI) or vice versa?

2) When I try running the analysis in QDEC as opposed to command line 
with mri_glmfit, I get very different results - I think because QDEC is 
generating different contrast files than the one specified in the paper 
(1 1 -1 -1 0). Basically, this seems to be due to the difference in 
modelling LGI with doss (command line) or dods (default QDEC). I was 
wondering whether there were any reason doss was chosen for LGI instead 
of dods (see Step 5 in Section 4 Statistical Group Comparisons)?

Thank you in advance for your help.

Kindest regards,
Colleen

-- 
Colleen Rollins, PhD Candidate
Department of Psychiatry
University of Cambridge
Herchel Smith Building, Robinson Way, Cambridge CB2 0SZ

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Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

2018-02-21 Thread Vanzo, Davide

Andrew,

Thank you for the confirmation.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu


On 2018-02-21 10:23:41-06:00 Hoopes, Andrew wrote:

Hi Davide,
Yes, the centos6 freesurfer6.0 download is compatible with centos7
best
Andrew



On February 20, 2018 at 5:59:04 PM, Vanzo, Davide 
(davide.va...@vanderbilt.edu) wrote:

Hello,

According from few messages in this mailing list, FreeSurfer 6.0.0 should be 
compatible with CentOS 7. However in the official documentation I cannot find 
any related statement. Moveover, the download web page still shows only CentOS 
6 as supported platform.

Could you please clarify if the current stable release works correctly on 
CentOS 7 or not?
Thank you.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu
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Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

2018-02-21 Thread Hoopes, Andrew

Hi Davide,

Yes, the centos6 freesurfer6.0 download is compatible with centos7

best
Andrew



On February 20, 2018 at 5:59:04 PM, Vanzo, Davide 
(davide.va...@vanderbilt.edu) wrote:

Hello,

According from few messages in this mailing list, FreeSurfer 6.0.0 should be 
compatible with CentOS 7. However in the official documentation I cannot find 
any related statement. Moveover, the download web page still shows only CentOS 
6 as supported platform.

Could you please clarify if the current stable release works correctly on 
CentOS 7 or not?
Thank you.

Best regards

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
www.accre.vanderbilt.edu
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[Freesurfer] Ask for unsubscribe from the mailinglist

2018-02-21 Thread Ying Wang

Hi,

Can I unsubscribe from the FreeSurfer mailing list?
My email address is: neuy...@gmail.com

Thanks!

Ying
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Re: [Freesurfer] Surface Errors

2018-02-21 Thread Bruce Fischl

Hi Emily

it is a segmentation error, but it's a pretty small one. It will mess up 
the thickness in a region a few mm^2. You could fix it by editing the 
wm.mgz if you really care about that spot

cheers
Bruce


On Wed, 21 Feb 2018, Emily Schwartz wrote:

> Hi Doug,
>
> Thank you for getting back to me. I've attached two images (Slice165 and 
> Slice166) with an arrow pointing to the location. I am new at this, so maybe 
> I am wrong and it is not a segmentation error.
>
> I've also attached an additional image (Slice185) of what I think is a type 
> of topological error that I often see multiple times in a subject. Is this a 
> topological defect? If so, if it is only over 3 slices does it need to be 
> corrected?
>
> Thanks again,
>
> Emily
> 
> 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, February 20, 2018 4:59 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Surface Errors
>
> sorry, what kind of errors? I could not really tell from the images what
> the problem was
>
>
> On 02/20/2018 10:22 AM, Emily Schwartz wrote:
>> Hi FreeSurfer community,
>>
>> I am working on elderly subjects and have had this kind of surface error 
>> quite often in different locations. Usually, it's over about 3-4 slices (in 
>> one view) and can be fixed, but I am finding multiple in almost every 
>> subject and therefore taking a lot of time to edit (and then once 
>> reprocessed new ones sometimes come up in different locations). I was 
>> wondering if these are normal to have, minor surface errors that do not 
>> necessarily need to be fixed. I have added images of an example below. Here 
>> are some of the values I get from aparc.stats for caudal middle frontal lh 
>> after manually editing:
>>
>> Surface area:
>> Original - 2500 mm^2
>> Edited -  2532 mm^2
>>
>> Grey volume:
>> Original -  1710 mm^3
>> Edited -  1727 mm^3
>>
>> Thickness avg
>> Original -  4455 mm  std: 2.371
>> Edited -  4445 mm  std: 2.365
>>
>> Although the thickness values only differ by 10 mm, we are a little 
>> concerned because the difference is not within the standard deviation.
>>
>> Please let me know if all of these errors should be edited or if it may be 
>> okay to keep the smaller segmentation/topological errors as they are.
>>
>> Thank you,
>>
>> Emily
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> 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] How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0 REPOST

2018-02-21 Thread Falk Lüsebrink

Hi Eric,

I think the easiest way to avoid N3 is to simply add the -nonuintensitycor flag 
to recon-all and create a symbolic link from nu.mgz to orig.mgz it as otherwise 
recon-all will end with an error. I'm not sure about the nomenclature of the T2 
file, but you should do the same.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 20. Februar 2018 17:17
An: Freesurfer support list
Betreff: Re: [Freesurfer] How would one run N4 bias corrected T1 and T2 images 
through FreeSurfer v6.0 REPOST

Hi Eric

the easiest thing would be to give your n4-corrected image to recon-all and let 
it run n3 on it. N3 is pretty gentle so I would think this would be fine. The 
alternative would be harder I think

cheers
Bruce

On Tue, 20 Feb 2018, Axelson, Eric D wrote:

> 
>  
> 
> We are using N4 to correct some large inhomogeneities in some samples 
> and wanted to insert these images into the v6.0 pipeline and bypass 
> the N3 bias correction done within.  What would be the correct 
> sequence of freesurfer commands to achieve this?  Thanks
> 
>  
> 
> Eric
> 
>  
> 
> 
> 
> __
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Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

2018-02-21 Thread zuxfoucault Wong

Attach name file and result file.

Thank you for your time!

Best,
Foucault

On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong 
wrote:

> Hi Kirstie,
>
> Thank you very much for the suggestions!
> I modified my snippet to prevent it from looping the same value and still
> got the same results?
>
> ##
> input=($(cat ./names_68parc.txt))
> labels=()
> hemis=()
> j=0
> for i in "${input[@]}"; do
> if [[ $i == lh_* ]]; then
> hemis[j]="lh"
> i=$(echo $i | sed 's/^lh_//g')
> labels[j]="$i"
> (( j++ ))
> elif [[ $i == rh_* ]]; then
> hemis[j]="rh"
> i=$(echo $i | sed 's/^rh_//g')
> labels[j]="$i"
> (( j++ ))
> fi
> done
>
> nlabel=68
> if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then
> echo " number of label not match "
> fi
>
>
> for hemi in lh rh; do
> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
> done
>
> for ((i=0;i<${#labels[@]};i++)); do
> mri_surfcluster --in 
> /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness
> --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum
> ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi
> ${hemis[i]} --subject fsaverage
> tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/  */ /g' | cut -d'
> ' -f6-8 >> ./labels/68parc.centroids.txt
> done
> ##
>
>
> The output message of mri_surfcluster:
> ##
> thsign = abs, id = 0
> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp
> $
> hemi   = rh
> srcid  = /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.
> thickness
> srcsubjid  = fsaverage
> srcsurf= white
> srcframe   = 0
> thsign = abs
> thmin  = 0
> thmax  = -1
> fdr= -1
> minarea= 0
> xfmfile= talairach.xfm
> clabelfile = ./labels/rh.lateraloccipital.label
> clabelinv  = 0
> nth = -1
> sumfile  = ./labels/sum.rh.lateraloccipital
> subjectsdir= /usr/local/freesurfer_orig/subjects
> FixMNI = 1
> Loading clabel ./labels/rh.lateraloccipital.label.
> Found 5963 points in clabel.
> - XFM matrix (RAS2RAS) ---
> /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm
>  1.0   0.0   0.0   0.0;
>  0.0   1.0   0.0   0.0;
>  0.0   0.0   1.0   0.0;
>  0.0   0.0   0.0   1.0;
> 
> Reading source surface /usr/local/freesurfer_orig/
> subjects/fsaverage/surf/rh.white
> Done reading source surface
> Computing metric properties
> Loading source values
> number of voxels in search space = 5963
> Done loading source values (nvtxs = 163842)
> overall max = 3.19752 at vertex 122846
> overall min = 0 at vertex 0
> surface nvertices 163842
> metric props tot surface area 65020.839844
> group_avg_vtxarea_loaded 1
> masked surface area 4459.747559
> NOT Adjusting threshold for 1-tailed test
> thminadj = 0
> Searching for Clusters ...
> thmin=0.00 (0.00), thmax=-1.00 (-1), thsignid=0,
> minarea=0.00
> Found 1 clusters
> Max cluster size 82167.00
> INFO: fixing MNI talairach coordinates
>
>
> On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker  wrote:
>
>> Hi Foucault,
>>
>> In the snippet you added you don’t define the labels variable (which you
>> subsequently loop over in for label in ${labels}).
>>
>> There are two possible mistakes that are easy to fix. One may be that you
>> forgot to read in the labels! And the other is that to get all the values
>> in an array you need ${labels[@]}.
>>
>> I don’t think you need greater precision than you have. The regions are
>> pretty far apart in mm terms :)
>>
>> Kirstie
>>
>> Sent from my iPhone, please excuse any typos or excessive brevity
>>
>> On 21 Feb 2018, at 03:44, zuxfoucault Wong  wrote:
>>
>> Dear Freesurfer experts,
>>
>> Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
>> 2013-September/07.html , I wrote a short script to extract the
>> centroids from Desikan-Killiany atlas.
>>
>> ##
>> for hemi in lh rh; do
>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
>> for label in ${labels}; do
>> mri_surfcluster --in /usr/local/freesurfer/subjects
>> /fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum
>> ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject
>> fsaverage
>> tail -1 ./labels/sum.${label} | sed 's/  */ /g' | cut -d' ' -f6-8 >>
>> ./labels/68parc.centroids.txt
>> done
>> done
>> ###
>>
>> However, 1) the value is not precise enough, it is only one digit after
>> decimal point. And 2) I kept getting the same value for each hemisphere.
>> Eg,.
>> 29.8 -20.7 18.0
>> 29.8 -20.7 18.0
>> 29.8 -20.7 18.0
>> 29.8 -20.7 18.0
>> 29.8 -20.7 18.0
>> 29.8 -20.7 18.0
>> 29.8 -20.7 18.0
>>
>> I would appreciate if you have any suggestions regarding extracting
>> centroids and the

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

2018-02-21 Thread zuxfoucault Wong

Hi Kirstie,

Thank you very much for the suggestions!
I modified my snippet to prevent it from looping the same value and still
got the same results?

##
input=($(cat ./names_68parc.txt))
labels=()
hemis=()
j=0
for i in "${input[@]}"; do
if [[ $i == lh_* ]]; then
hemis[j]="lh"
i=$(echo $i | sed 's/^lh_//g')
labels[j]="$i"
(( j++ ))
elif [[ $i == rh_* ]]; then
hemis[j]="rh"
i=$(echo $i | sed 's/^rh_//g')
labels[j]="$i"
(( j++ ))
fi
done

nlabel=68
if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then
echo " number of label not match "
fi


for hemi in lh rh; do
mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
done

for ((i=0;i<${#labels[@]};i++)); do
mri_surfcluster --in
/usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness
--clabel ./labels/${hemis[i]}.${labels[i]}.label --sum
./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi
${hemis[i]} --subject fsaverage
tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/  */ /g' | cut -d' '
-f6-8 >> ./labels/68parc.centroids.txt
done
##


The output message of mri_surfcluster:
##
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $
hemi   = rh
srcid  =
/usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.thickness
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = abs
thmin  = 0
thmax  = -1
fdr= -1
minarea= 0
xfmfile= talairach.xfm
clabelfile = ./labels/rh.lateraloccipital.label
clabelinv  = 0
nth = -1
sumfile  = ./labels/sum.rh.lateraloccipital
subjectsdir= /usr/local/freesurfer_orig/subjects
FixMNI = 1
Loading clabel ./labels/rh.lateraloccipital.label.
Found 5963 points in clabel.
- XFM matrix (RAS2RAS) ---
/usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Reading source surface
/usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.white
Done reading source surface
Computing metric properties
Loading source values
number of voxels in search space = 5963
Done loading source values (nvtxs = 163842)
overall max = 3.19752 at vertex 122846
overall min = 0 at vertex 0
surface nvertices 163842
metric props tot surface area 65020.839844
group_avg_vtxarea_loaded 1
masked surface area 4459.747559
NOT Adjusting threshold for 1-tailed test
thminadj = 0
Searching for Clusters ...
thmin=0.00 (0.00), thmax=-1.00 (-1), thsignid=0,
minarea=0.00
Found 1 clusters
Max cluster size 82167.00
INFO: fixing MNI talairach coordinates


On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker  wrote:

> Hi Foucault,
>
> In the snippet you added you don’t define the labels variable (which you
> subsequently loop over in for label in ${labels}).
>
> There are two possible mistakes that are easy to fix. One may be that you
> forgot to read in the labels! And the other is that to get all the values
> in an array you need ${labels[@]}.
>
> I don’t think you need greater precision than you have. The regions are
> pretty far apart in mm terms :)
>
> Kirstie
>
> Sent from my iPhone, please excuse any typos or excessive brevity
>
> On 21 Feb 2018, at 03:44, zuxfoucault Wong  wrote:
>
> Dear Freesurfer experts,
>
> Based on this https://mail.nmr.mgh.harvard.edu/pipermail//
> freesurfer/2013-September/07.html , I wrote a short script to extract
> the centroids from Desikan-Killiany atlas.
>
> ##
> for hemi in lh rh; do
> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
> for label in ${labels}; do
> mri_surfcluster --in 
> /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness
> --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid
> --thmin 0 --hemi ${hemi} --subject fsaverage
> tail -1 ./labels/sum.${label} | sed 's/  */ /g' | cut -d' ' -f6-8 >>
> ./labels/68parc.centroids.txt
> done
> done
> ###
>
> However, 1) the value is not precise enough, it is only one digit after
> decimal point. And 2) I kept getting the same value for each hemisphere.
> Eg,.
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
>
> I would appreciate if you have any suggestions regarding extracting
> centroids and the aforementioned issues!
> Thank you for your time!
>
> Best,
> Foucault
>
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