date:20170912

Re: [Freesurfer] Results display tool

2017-09-12 Thread Chris Adamson

Fixed. Forgot to upload some files. Thanks Doug.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, 13 September 2017 2:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Results display tool

Thanks Chris,  this looks interesting and useful. I just tried

|P = cell(1, 2); T = cell(1, 2); for z = 1:2 P{z} = rand(31, 1) * 0.075;
T{z} = rand(31, 1) * 5 - 3; end freesurfer_statsurf_p(P, T, 'dkt'); and got the 
error: Undefined function 'freesurfer_read_annot' for input arguments of type 
'char'. Error in freesurfer_statsurf_loadsurfaces (line 59) [~, 
AnnotLabel{HemiIDX}, AnnotTable{HemiIDX}] = 
freesurfer_read_annot(fullfile(FreesurferSubjectsDir, 'fsaverage', 'label', 
[Hemi '.' LabelName '.annot'])); Error in freesurfer_statsurf_checkargs (line 
104) [FSAverageV, FSAverageF, ValueVertexIDX, RGB] = 
freesurfer_statsurf_loadsurfaces(SurfType,
FreesurferSeedType); Error in freesurfer_statsurf_p (line 45) [GroupLabels, ... 
anything I'm doing wrong? Welcome to the fun world of supporting software you 
provide for free! doug |


On 09/12/2017 05:31 AM, Chris Adamson wrote:
>
> Freesurfer users,
>
> I just wanted to advertise a set of display tools that I wrote for 
> easy display, in MATLAB, of regional stats like p-values/effect 
> sizes/arbitrary scalars with customisable masks for aparc, dkt, 
> aparc.a2009s.
>
> https://chrisadamsonmcri.github.io/freesurfer_statsurf_display
>
> I hope people find it useful.
>
> Chris.
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Resampling Freesurfer - Human connectome workbench

2017-09-12 Thread Douglas N Greve

Try something like


mris_convert -c myfile.w lh.white myfile.gii


if the .w file does not work, then use the mgh file


On 09/12/2017 07:13 PM, Xavier Guell Paradis wrote:
> Dear freesurfer experts,
>
> I have an overlay freesurfer file (format is .w) which corresponds to 
> a thresholded seed-based functional connectivity surface map (group 
> result). The .w file was generated from an SPM analysis, following the 
> instructions described here 
> (http://spmsurfrend.sourceforge.net/Documentation/SPM_SurfRend_Tutorial_V0.2.1.pdf).
> I have one .w file for each cerebral hemisphere. I would like to 
> visualize these .w maps using workbench_view, and I have tried to 
> follow the instructions the HCP team published here 
> (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?).
> As a first step I would need to convert the .w files into .func.gii 
> files using mris_convert. Then I would use wb_command 
> -metric-resample, as indicated in the instructions. This does not seem 
> to work with my .w file:
>
> 1) mris_convert myfile.w myfile.func.gii
> This generates myfile.func.gii, but when I use wb_command 
> -metric-resample I get the following error:
> *ERROR: Parse error while reading: error occurred while parsing 
> element, line number: 1 column number: 1*
>
> 2) As an alternative approach, I opened myfile.w using Tksurfer and 
> saved the overlay (myfile.w) with .mgh format (generating a new file: 
> "myfile.mgh"). Then I do the following:
> mris_convert myfile.mgh myfile.func.gii
> This generates the myfile.func.gii file, but when I use wb_command 
> -metric-resample with this file I get a different error:
> *ERROR: All data arrays (columns) in the file must have the same 
> number of rows.  The first array (column) contains 163842 rows.  Array 
> 2 contains 327680 rows.*
>
> I have asked the HCP team, but they were not familiar with the .w 
> files and suggested that I ask you instead.
>
> Thank you very much for your help,
> Xavier.
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Resampling Freesurfer - Human connectome workbench

2017-09-12 Thread Xavier Guell Paradis

Dear freesurfer experts,

I have an overlay freesurfer file (format is .w) which corresponds to a
thresholded seed-based functional connectivity surface map (group result). The
.w file was generated from an SPM analysis, following the instructions
described here
(http://spmsurfrend.sourceforge.net/Documentation/SPM_SurfRend_Tutorial_V0.2.1.pdf).
I have one .w file for each cerebral hemisphere. I would like to visualize
these .w maps using workbench_view, and I have tried to follow the instructions
the HCP team published here
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?).
As a first step I would need to convert the .w files into .func.gii files using
mris_convert. Then I would use wb_command -metric-resample, as indicated in the
instructions. This does not seem to work with my .w file:

1) mris_convert myfile.w myfile.func.gii
This generates myfile.func.gii, but when I use wb_command -metric-resample I
get the following error:
ERROR: Parse error while reading: error occurred while parsing element, line
number: 1 column number: 1

2) As an alternative approach, I opened myfile.w using Tksurfer and saved the
overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then
I do the following:
mris_convert myfile.mgh myfile.func.gii
This generates the myfile.func.gii file, but when I use wb_command
-metric-resample with this file I get a different error:
ERROR: All data arrays (columns) in the file must have the same number of rows.
The first array (column) contains 163842 rows. Array 2 contains 327680 rows.

I have asked the HCP team, but they were not familiar with the .w files and
suggested that I ask you instead.

Thank you very much for your help,
Xavier.
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Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Douglas N Greve

CSFVol is actually the volume of the CSF label (index 24)

3rd4th5thCSF is the volume of the 3rd, 4th, 5th ventricles plus the CSF 
label

VentChorVol is the volume of choroird plexus, lateral ventricles, and 
inferior lateral ventricles

   BrainSegVolNotVent = BrainSegVol - VentChorVol - 3rd4th5thCSF ;



On 09/12/2017 02:13 PM, Benjamin Luerweg wrote:
> Hey Mr. Greve,
>
> thank your very much again!
> if i understand you right, the inside the console shown up values 
> can’t be extracted into a separate file?
>
> beside that, this values are of interest for me, so that i copied them 
> to a text file.
> as you can see:Getting Brain Volume Statistics
> ...
> SubCortGMVol 56306.000
> SupraTentVol 963813.403 (960508.000) diff=3305.403 pctdiff=0.343
> SupraTentVolNotVent 940278.403 (936973.000) diff=3305.403 pctdiff=0.352
> BrainSegVol 1109500.000 (1106935.000) diff=2565.000 pctdiff=0.231
> BrainSegVolNotVent 1082437.000 (1082065.403) diff=371.597 pctdiff=0.034
> BrainSegVolNotVent 1082437.000
> CerebellumVol 145310.000
> VentChorVol   23535.000
> 3rd4th5thCSF   3528.000
> CSFVol   963.000,
> OptChiasmVol   154.000
> MaskVol 1526326.000
>
> am i right that this CSFVol is the Volume of all ventricles not including
> the extra cerebral CSF?
> i tried to calculate the CSFVol reverse by calculating: VentChorVol - 
> Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this?
>
> and what exactly is the VentChorVol and 3rd4th5thCSF for?
>
> im a bit confused about all this lables and im sorry for asking you so 
> much but i would really appreciate to solve this pity situation.
>
> do you have a kind of an overview?
>
> thank you in advance again,
>
> ben luerweg
>
>
>
>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve 
>> >:
>>
>>
>>
>> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
>>> dear fs community,
>>>
>>> as a kind of a freesurfer greenhorn i would kindly ask you to help me
>>> out with identifying the different labels used by freesurfer.
>>> after using mri segstats most of the labels seem to be describing
>>> thereselfs in proper way.
>>>
>>> what i don’t understand are for example the different volume values
>>> showing up inside the console after entering the segstat command.
>>>
>>> VentChorVol what does this label explain?
>> Volume of all ventricles plus the volume of the chorioid plexus.
>>>
>>> CSFVolwhy is this volume differing to the one within the segstat file?
>> Volume of all ventricles (not well named because it does not include
>> extra cerebral CSF)
>>>
>>> and finally i would really love to know how to calculate a correct
>>> brain to liquor ratio?!
>> Do you mean brain volume to total CSF volume? See above
>>>
>>>
>>> kind regards,
>>> ben
>>>
>>>
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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.
>>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] glmfit: matrix error

2017-09-12 Thread Douglas N Greve

If you seek help with this problem, make sure to send:


On 09/12/2017 02:51 PM, Wang, Xin wrote:
>
> Hello, FreeSurfer group,
>
> When I ran glmfit I got the following error massage. I standardize 
> ages but the problem remains. Any other suggestions? Alternatively, is 
> there any way to by-pass this design checking step?
>
> Thank you very much.
>
> Xin
>
> 
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>
> 
>
> Possible problem with experimental design:
>
> Check for duplicate entries and/or lack of range of
>
> continuous variables within a class.
>
> If you seek help with this problem, make sure to send:
>
>   1. Your command line:
>
> mri_glmfit.bin --y 
> RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh_group_currPTSD_AgeGenderSiteFACT_adult.fwhm10.fsaverage.mgh
>  
> --fsgd group_currPTSD_AgeGenderSiteFACT_adult.fsgd dods --glmdir 
> RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh --surf fsaverage/ lh 
> --C group_currPTSD_AgeGenderSiteFACT_adult.mtx
>
>   2. The FSGD file (if using one)
>
>   3. And the design matrix above
>
> Attempting to diagnose further
>
> SumSq: Min=0.33 (col 38), Max=18.703472 (col 62)
>
> The scale is much different between columns 38 and 62, you may want to
>
>  normalize by subtracting the mean and dividing by the standard deviation.
>
> ERROR: cannot find 
> RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh/fwhm.dat
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Q re: cluster commands

2017-09-12 Thread Douglas N Greve



On 09/12/2017 03:50 PM, Omar Al-Louzi wrote:
>
> Hi freesurfer team,
>
> I’m hoping to ask two questions:
>
>  1. We are using the mri_volcluster command to find manually
> delineated clusters in a volume. In the output file, the command
> outputs Talairach coordinates for each cluster (TalX, TalY, TalZ).
> What do these coordinates exactly correspond to in terms of
> voxels? (i.e. do they reference the central voxel of each cluster,
> the first voxel detected, or something else)
>
The location of the maximum in the cluster.
>
> 1.
>
>
>  2. Are there any freesurfer command(s) that can measure the minimum
> distance between two clusters in the same volume, or measure the
> minimum distance between one cluster in one volume( let’s call it
> reference cluster) and multiple clusters in a second volume,
> granted that both volumes are in the same space and registered to
> each other (in other words, generate minimum distance measurements
> between all the clusters in the second volume and the reference
> cluster in the first volume).
>
No, sorry
>
> 2.
>
> My apologies if these questions are basic or have been asked before, 
> but I haven’t come across an answer on freesurfer forums or help files.
>
> Best,
>
> Omar
>
> 
>
> Omar Al-Louzi, MD
>
> PGY-3 Neurology resident
>
> Massachusetts General Hospital
>
> Brigham and Women’s hospital
>
>
>
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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
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[Freesurfer] Q re: cluster commands

2017-09-12 Thread Omar Al-Louzi

Hi freesurfer team,

 

I'm hoping to ask two questions:

 

1.  We are using the mri_volcluster command to find manually delineated
clusters in a volume. In the output file, the command outputs Talairach
coordinates for each cluster (TalX, TalY, TalZ). What do these coordinates
exactly correspond to in terms of voxels? (i.e. do they reference the
central voxel of each cluster, the first voxel detected, or something else)

 

2.  Are there any freesurfer command(s) that can measure the minimum
distance between two clusters in the same volume, or measure the minimum
distance between one cluster in one volume( let's call it reference cluster)
and multiple clusters in a second volume, granted that both volumes are in
the same space and registered to each other (in other words, generate
minimum distance measurements between all the clusters in the second volume
and the reference cluster in the first volume).

 

My apologies if these questions are basic or have been asked before, but I
haven't come across an answer on freesurfer forums or help files.

 

Best,

Omar

  _  

Omar Al-Louzi, MD

PGY-3 Neurology resident

Massachusetts General Hospital

Brigham and Women's hospital

 

 

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[Freesurfer] glmfit: matrix error

2017-09-12 Thread Wang, Xin

Hello, FreeSurfer group,

When I ran glmfit I got the following error massage. I standardize ages but the
problem remains. Any other suggestions? Alternatively, is there any way to
by-pass this design checking step?

Thank you very much.

Xin

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
1. Your command line:
mri_glmfit.bin --y
RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh_group_currPTSD_AgeGenderSiteFACT_adult.fwhm10.fsaverage.mgh
--fsgd group_currPTSD_AgeGenderSiteFACT_adult.fsgd dods --glmdir
RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh --surf fsaverage/ lh --C
group_currPTSD_AgeGenderSiteFACT_adult.mtx
2. The FSGD file (if using one)
3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.33 (col 38), Max=18.703472 (col 62)
The scale is much different between columns 38 and 62, you may want to
normalize by subtracting the mean and dividing by the standard deviation.
ERROR: cannot find RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh/fwhm.dat

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Re: [Freesurfer] (no subject)

2017-09-12 Thread José Gómez-Feria Ferreiro

El El mar, 12 sept 2017 a las 20:19, José Gómez-Feria Ferreiro <
josegomezfe...@gmail.com> escribió:

> Dear Freesurfer,
>
> Is it possible to keep on the supporting list but without receiving emails
> from other people? My email account is getting stuck with so many emails.
>
> Thanks,
>
> Jose
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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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[Freesurfer] (no subject)

2017-09-12 Thread José Gómez-Feria Ferreiro

Dear Freesurfer,

Is it possible to keep on the supporting list but without receiving emails
from other people? My email account is getting stuck with so many emails.

Thanks,

Jose
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Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Benjamin Luerweg

Hey Mr. Greve,

thank your very much again!
if i understand you right, the inside the console shown up values can’t be 
extracted into a separate file?

beside that, this values are of interest for me, so that i copied them to a 
text file.

as you can see: Getting Brain Volume Statistics
...
SubCortGMVol  56306.000
SupraTentVol  963813.403 (960508.000) diff=3305.403 
pctdiff=0.343
SupraTentVolNotVent  940278.403 (936973.000) 
diff=3305.403 pctdiff=0.352
BrainSegVol  1109500.000 (1106935.000) diff=2565.000 
pctdiff=0.231
BrainSegVolNotVent  1082437.000 (1082065.403) 
diff=371.597 pctdiff=0.034
BrainSegVolNotVent  1082437.000
CerebellumVol 145310.000
VentChorVol   23535.000
3rd4th5thCSF   3528.000
CSFVol   963.000, 
OptChiasmVol   154.000
MaskVol 1526326.000

am i right that this CSFVol is the Volume of all ventricles not including
the extra cerebral CSF?
i tried to calculate the CSFVol reverse by calculating: VentChorVol - 
Choroidplexus(2*) = ..and it didn’t fit with the CSFVol?! why this?

and what exactly is the VentChorVol and 3rd4th5thCSF for?

im a bit confused about all this lables and im sorry for asking you so much but 
i would really appreciate to solve this pity situation.

do you have a kind of an overview?

thank you in advance again,

ben luerweg



> Am 11.09.2017 um 22:01 schrieb Douglas N Greve :
> 
> 
> 
> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
>> dear fs community,
>> 
>> as a kind of a freesurfer greenhorn i would kindly ask you to help me 
>> out with identifying the different labels used by freesurfer.
>> after using mri segstats most of the labels seem to be describing 
>> thereselfs in proper way.
>> 
>> what i don’t understand are for example the different volume values 
>> showing up inside the console after entering the segstat command.
>> 
>> VentChorVol what does this label explain?
> Volume of all ventricles plus the volume of the chorioid plexus.
>> 
>> CSFVolwhy is this volume differing to the one within the segstat file?
> Volume of all ventricles (not well named because it does not include 
> extra cerebral CSF)
>> 
>> and finally i would really love to know how to calculate a correct 
>> brain to liquor ratio?!
> Do you mean brain volume to total CSF volume? See above
>> 
>> 
>> kind regards,
>> ben
>> 
>> 
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> -- 
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> MGH-NMR Center
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> Phone Number: 617-724-2358
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Re: [Freesurfer] group analysis on thickness/mask

2017-09-12 Thread Douglas N Greve

Pass it with --mask, not --label


On 09/11/2017 09:42 PM, Xianwei Che wrote:
> Dear Doug,
>
> After some trial and error I am still not able to run group analysis 
> in ROI manner.
>
> Here is my understanding: I need to define a label (mri_binarize ?) in 
> which my ROIs should be labeled as 1 with other regions being 0. Then 
> I can take this label to glm with --lable and then run correction. If 
> this is a right way can you tell me a little bit more of how to do 
> this. I am working on cortical thickness data.
>
> Thanks huge
>
>
>
> /-/
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
> On 12 September 2017 at 08:42, Xianwei Che  > wrote:
>
> Dear Doug,
>
> Thank you for the answer. I will try it out.
>
> Regards
>
> /-/
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
> On 12 September 2017 at 01:44, Douglas N Greve
> > wrote:
>
>
>
> On 09/10/2017 04:02 AM, Xianwei Che wrote:
> > Dear experts,
> >
> > I am going to run a group analysis on thickness but limit
> the results
> > to certain regions, say prefrontal cortex. l did find this
> thread but
> > failed to make it work on my data
> >
> 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html
> 
> ).
> > I know I could extract the signal of the ROI but also
> interested in
> > this way.
> >
> > Here are my questions:
> > 1. mri_binarize should be working on the average data or the
> single
> > data in each participant. If it should be on individual
> data, what the
> > loop should be (if I have a text file SUBJECTS listing the
> participants).
> Actually, I don't know what [subjects] is supposed to mean.
> You should
> include the index for the ROIs you want in the analysis
> > 2. How the --match is used. I --helped the mri_binarize but did not
> > get it. Is it for specifying the ROI by number, say the
> number of PFC?
> There is no PFC ROI. You will have to piece it together from
> other ROIs.
> You can get the full list from
> $FREESURFER_HOME/FreeSurferColorLUT.txt.
> Look in the section for aparc+aseg.mgz
> > 3. If I could finish the mask creation and merge to label; do I have
> > to undergo the data concatenating stage (i.e. preproc,
> surf2surf) or
> > directly move to glm. I saw another thread skipping these
> stages but
> > it's on volume data
> >
> 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html
> 
> ).
> Yu can move directly to the GLM
> >
> > Thank you so much!
> >
> >
> > /-/
> > Mr Xianwei Che
> > PhD Candidate
> > Monash Alfred Psychiatry Research Centre (MAPrc)
> > Central Clinical School & the Alfred
> > Monash University
> > Level 4, 607 St Kilda Road, Melbourne 3004, Australia
> >
> >
> > ___
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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
> 
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> 
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> 
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> 
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Re: [Freesurfer] Results display tool

2017-09-12 Thread Douglas N Greve

Thanks Chris,  this looks interesting and useful. I just tried

|P = cell(1, 2); T = cell(1, 2); for z = 1:2 P{z} = rand(31, 1) * 0.075; 
T{z} = rand(31, 1) * 5 - 3; end freesurfer_statsurf_p(P, T, 'dkt'); and 
got the error: Undefined function 'freesurfer_read_annot' for input 
arguments of type 'char'. Error in freesurfer_statsurf_loadsurfaces 
(line 59) [~, AnnotLabel{HemiIDX}, AnnotTable{HemiIDX}] = 
freesurfer_read_annot(fullfile(FreesurferSubjectsDir, 'fsaverage', 
'label', [Hemi '.' LabelName '.annot'])); Error in 
freesurfer_statsurf_checkargs (line 104) [FSAverageV, FSAverageF, 
ValueVertexIDX, RGB] = freesurfer_statsurf_loadsurfaces(SurfType, 
FreesurferSeedType); Error in freesurfer_statsurf_p (line 45) 
[GroupLabels, ... anything I'm doing wrong? Welcome to the fun world of 
supporting software you provide for free! doug |


On 09/12/2017 05:31 AM, Chris Adamson wrote:
>
> Freesurfer users,
>
> I just wanted to advertise a set of display tools that I wrote for 
> easy display, in MATLAB, of regional stats like p-values/effect 
> sizes/arbitrary scalars with customisable masks for aparc, dkt, 
> aparc.a2009s.
>
> https://chrisadamsonmcri.github.io/freesurfer_statsurf_display
>
> I hope people find it useful.
>
> Chris.
>
>
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Re: [Freesurfer] PetSurfer GTM: gtmstats2table

2017-09-12 Thread Douglas N Greve

what is the nature of the customization? Ie, do you want to customize 
cortical, subcortical, or WM? For cortical, you will have to specify a 
different annotation with --ctx-annot when running gtmseg (and specify 
--o to call it a different name). You may have to update the lookup 
table generated by gtmseg to indicate the tissue type of any new 
parcellations. Then just run mri_gtmpvc specifying the new gtmseg


On 09/12/2017 12:30 PM, Elijah Mak wrote:
> Hi Doug,
>
> Thanks for the clarification. According to the PetSurfer guide, it is 
> stated that there are “ways to customise this segmentation to use ROI 
> definitions”. How may I go about doing that? Appreciate your help.
>
> Best Wishes,
> Elijah
>
> *Dr. Elijah Mak, Research Associate
> *Department of Psychiatry
> Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
> Disabilities Research Group
> University of Cambridge,
> Trinity College, CB21TQ, UK
> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24
>
>
> On 12 September 2017 at 17:27:10, Douglas N Greve 
> (gr...@nmr.mgh.harvard.edu ) wrote:
>
>> what do you mean? You can only get gtm stats from the parcellations that
>> you have used during the process. You can't get new values at the end.
>> If you want to use different ROIs, then you need to run gtmseg again
>> with a different parcellation, then run mri_gtmpvc with the new gtmseg
>>
>>
>> On 09/12/2017 10:42 AM, Elijah Mak wrote:
>> > Hi Doug,
>> >
>> > Would it be possible to use the gtmstats2table command to extract GTM
>> > values from other parellations?
>> >
>> > Thanks!
>> >
>> > Best Wishes,
>> > Elijah
>> >
>> >
>> > *Dr. Elijah Mak, Research Associate
>> > *Department of Psychiatry
>> > Old Age Psychiatry Group | Cambridge Intellectual & Developmental
>> > Disabilities Research Group
>> > University of Cambridge,
>> > Trinity College, CB21TQ, UK
>> > http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24
>> >
>> >
>> >
>> > ___
>> > 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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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] lobes volume (WM and GM)

2017-09-12 Thread Bruce Fischl


Hi Gonzalo

I don't think "wm for a lobe" is well-defined once you get into the deep 
wm

Bruce
On Tue, 12 Sep 2017, Gonzalo Rojas Costa wrote:


Hi:

 I need the complete WM volume for each lobe... not only the WM up to
5mm beneath the lobes (default value) or 20 mm...

 Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
http://www.aribrain.info
https://scholar.google.com/citations?user=LO7LZ3oJ
https://www.researchgate.net/profile/Gonzalo_Rojas2
https://cl.linkedin.com/in/gonzalorojascosta

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Re: [Freesurfer] lobes volume (WM and GM)

2017-09-12 Thread Douglas N Greve

Try removing the --rip-unknown


On 09/12/2017 11:09 AM, Gonzalo Rojas Costa wrote:
> Hi:
>
>I created the following script (for freesurfer 5.3.0) to compute the
> lobes volume (including GM and WM).
>
>mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos
> --seg lobulos --stat lobulos
>mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos
> --seg lobulos --stat lobulos
>mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh
>mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh
>mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown
> --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos
> --wmparc-dmax 20
>mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab
> /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum
> $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001
> 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255
>
>But, I didn't got the complete WM volume for each lobe (frontal lobe
> for example... see red arrow in attached image)... why ?... Any
> solution ?...
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
> http://www.aribrain.info
> https://scholar.google.com/citations?user=LO7LZ3oJ
> https://www.researchgate.net/profile/Gonzalo_Rojas2
> https://cl.linkedin.com/in/gonzalorojascosta
>
>
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[Freesurfer] lobes volume (WM and GM)

2017-09-12 Thread Gonzalo Rojas Costa

Hi:

  I need the complete WM volume for each lobe... not only the WM up to
5mm beneath the lobes (default value) or 20 mm...

  Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
http://www.aribrain.info
https://scholar.google.com/citations?user=LO7LZ3oJ
https://www.researchgate.net/profile/Gonzalo_Rojas2
https://cl.linkedin.com/in/gonzalorojascosta

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Re: [Freesurfer] PetSurfer GTM: gtmstats2table

2017-09-12 Thread Elijah Mak

Hi Doug,

Thanks for the clarification. According to the PetSurfer guide, it is stated 
that there are “ways to customise this segmentation to use ROI definitions”. 
How may I go about doing that? Appreciate your help.

Best Wishes,
Elijah 

Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge,
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

On 12 September 2017 at 17:27:10, Douglas N Greve (gr...@nmr.mgh.harvard.edu) 
wrote:

what do you mean? You can only get gtm stats from the parcellations that  
you have used during the process. You can't get new values at the end.  
If you want to use different ROIs, then you need to run gtmseg again  
with a different parcellation, then run mri_gtmpvc with the new gtmseg  

On 09/12/2017 10:42 AM, Elijah Mak wrote:  
> Hi Doug,  
>  
> Would it be possible to use the gtmstats2table command to extract GTM  
> values from other parellations?  
>  
> Thanks!  
>  
> Best Wishes,  
> Elijah  
>  
>  
> *Dr. Elijah Mak, Research Associate  
> *Department of Psychiatry  
> Old Age Psychiatry Group | Cambridge Intellectual & Developmental  
> Disabilities Research Group  
> University of Cambridge,  
> Trinity College, CB21TQ, UK  
> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24  
>  
>  
>  
> ___  
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--  
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MGH-NMR Center  
gr...@nmr.mgh.harvard.edu  
Phone Number: 617-724-2358  
Fax: 617-726-7422  

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Re: [Freesurfer] QDEC FDR for left and right hemispheres

2017-09-12 Thread Douglas N Greve



On 09/12/2017 10:45 AM, Huang, Caleb (NIH/NINDS) [F] wrote:
>
> Hello,
>
>
> When I run FDR on QDEC, I get different p-values for the left and 
> right hemispheres. Is it appropriate to use just one threshold for the 
> sake of consistency?
>
Probably so. There is not a way to do this from qdec. You can use 
mri_fdr to get the appropriate thershold, and then plug that into qdec.
>
>
> Also, as an unrelated question, is there a way to display the 
> thresholds as p-values rather than log(p)?
>
No, not in qdec at least

>
> -Caleb
>
>
>
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Re: [Freesurfer] PetSurfer GTM: gtmstats2table

2017-09-12 Thread Douglas N Greve

what do you mean? You can only get gtm stats from the parcellations that 
you have used during the process. You can't get new values at the end. 
If you want to use different ROIs, then you need to run gtmseg again 
with a different parcellation, then run mri_gtmpvc with the new gtmseg

On 09/12/2017 10:42 AM, Elijah Mak wrote:
> Hi Doug,
>
> Would it be possible to use the gtmstats2table command to extract GTM 
> values from other parellations?
>
> Thanks!
>
> Best Wishes,
> Elijah
>
>
> *Dr. Elijah Mak, Research Associate
> *Department of Psychiatry
> Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
> Disabilities Research Group
> University of Cambridge,
> Trinity College, CB21TQ, UK
> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24
>
>
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Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Douglas N Greve



On 09/12/2017 09:06 AM, Benjamin Luerweg wrote:
> dear mr. Greve,
> dear fs community,
>
> first of all thank you very much for helping me so far.
>
> what i don’t understand is the difference between the value *CSF* 
> (within the aseg.stat) and the *CSFVol* which shows up inside
> the console while processing the command to generate the aseg.stat file.
The "CSF" label is a small ROI of CSF that did not fit into any of the 
standard ventricle definitions. It is not well-named and creates confusion.
>
> additional to this i would like to know why some of this values 
> directly showing up inside the console are not included/part of the 
> final aseg.stat?!
> is there a different way to get a file which includes this 
> morphometric data?
> (because like i told you: for example the aseg.stat value CSF differs 
> from the inside the console shown value CSFVol (which is not part of 
> aseg))
There is not a way to get the data from the console. However, you can 
compute *BrainSeg-**BrainSegNotVent to get venticular CSF volume
*
>
> regarding to this ratio which i need its the *VBR* i meant 
> (https://en.wikipedia.org/wiki/Ventricular-brain_ratio)
> whats the *best way to calculate this value?* which parameters should 
> i use?
Not sure. I guess it would be CSFVol/BrainSeg or CSFVol/BrainSegNotVent
>
> my last question is about how to calculate the whole corpus calosum 
> volume - is it possible to add all CC values to a value for the 
> complete CC?
I'm not sure that CC "volume" is meaningful since the CC is not really a 
3D structure. Maybe you want to use CC surface area?
>
>
> thank your very much in advance,
> benjamin luerweg
>
> _
>
>
>
>> Am 11.09.2017 um 22:01 schrieb Douglas N Greve 
>> >:
>>
>>
>>
>> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
>>> dear fs community,
>>>
>>> as a kind of a freesurfer greenhorn i would kindly ask you to help me
>>> out with identifying the different labels used by freesurfer.
>>> after using mri segstats most of the labels seem to be describing
>>> thereselfs in proper way.
>>>
>>> what i don’t understand are for example the different volume values
>>> showing up inside the console after entering the segstat command.
>>>
>>> VentChorVol what does this label explain?
>> Volume of all ventricles plus the volume of the chorioid plexus.
>>>
>>> CSFVolwhy is this volume differing to the one within the segstat file?
>> Volume of all ventricles (not well named because it does not include
>> extra cerebral CSF)
>>>
>>> and finally i would really love to know how to calculate a correct
>>> brain to liquor ratio?!
>> Do you mean brain volume to total CSF volume? See above
>>>
>>>
>>> kind regards,
>>> ben
>>>
>>>
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>>
>> -- 
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>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
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Re: [Freesurfer] side effects launching recon-all from matlab system(cmd) call

2017-09-12 Thread Douglas N Greve

when you run an external command from matalb, it starts a new shell, and 
that shell will have an environment. It looks like the env is different 
than when you run something from a standard shell. Eg, when you open a 
bash shell, do you  source the freesurfer environment before running FS 
commands? If so, you'd need to do the same thing in the shell  created 
by matlab to get the same result


On 09/12/2017 04:24 AM, Giuseppe Cabras wrote:
> Thanks Douglas for your reply.
>
> I checked in detail the talairach_avi.log files and they show that 
> imgreg_4dfp c executable:
>
> $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $
>
> are executed in both environment (bash and matlab), but in bash 
> imgreg_4dfp call in turn
>
> $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $
>
> that show eta,q values in the talairach_avi.log file. Seems to me 
> that, if I call recon-all from matlab, fimgreg code ( which I don't 
> know where it is) is not executed or it don't write results to 
> talairach_avi.log output, but probably talairach avi transform is fine.
>
> ... very strange behaviour.
>
> Cheers,
>
> Giuseppe
>
>
> On 11/09/2017 18:25, Douglas N Greve wrote:
>>The tal_QC_AZS scripts expects the log file to have a specific 
>> format,
>> and it looks like something changes when you run it inside matlab.
>> sorry, the only idea I have is that the linux environments might be
>> different in bash vs matlab.
>>
>>
>> On 09/11/2017 08:25 AM, Giuseppe Cabras wrote:
>>> Dear freesurfer developers,
>>>
>>> I call recon-all -all from a matlab script using a system(cmd) which
>>> is (apparently) correctly executed, as shown in the recon-all.log
>>> (matlab_* attached), i.e.:
>>>
>>> /usr/local/freesurfer/bin/recon-all
>>> -all -cw256 -3T -multistrip -clean-bm -i
>>> /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s
>>> /home/gc/study/recon-all/400614dclass
>>>
>>> and apparently it run without errors as you can see in the
>>> matlab_recon-all.log file, but I get (systematically) a wrong
>>>
>>> TalAviQA: 0.0
>>>
>>> while, if I run the above bash command directly I get a correct:
>>>
>>> TalAviQA: 0.97713
>>>
>>> as shown in the bash_recon-all.log (attached). I guessed that
>>> something wrong happened  in
>>>
>>>   talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>> --atlas 3T18yoSchwartzReactN32_as_orig
>>>
>>> and the error traced in talairach_avi.log (matlab_* and bash_*
>>> attached). In fact matlab_talairach_avi.log is shorter and all
>>> imgreg_4dfp end sections are missing which imply that TalAviQA can not
>>> be extracted by awk and mritotal transform is performed instead. But
>>> really I don't understand why this happens and whether similar issues
>>> affects other recon-all subtask using matlab. I double checked this on
>>> two linux sistems and with fs version 6.0 and 5.3 ... same results.
>>>
>>> Thanks in advance for any help,
>>>
>>> cheers,
>>>
>>>
>>>
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Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

2017-09-12 Thread Douglas N Greve

Do you mean that the error is still there even after running the 
unsetenv command? And you ran them from the shell, one after the other?


On 09/12/2017 02:27 AM, M Janani wrote:
> Hi Douglas,
>
>   We tried running this command. But command not found error.
>
> Thanks,
> Janani
>   
>
>   
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 12 September 2017 01:25
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault
>
> Try running
>
> unsetenv FS_LOAD_DWI
>
>
> then re-running recon-all
>
> On 09/11/2017 12:57 PM, M Janani wrote:
>> Hi Team,
>>
>>  Am getting segmentation error during the
>> reconstruction process.
>>
>>  Please help in resolving the error.
>>
>>  I have attached log for reference.
>>
>> Thanks,
>>
>> Janani
>>
>>
>>
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[Freesurfer] FS6.0 on RHEL7 FIPS enabled - ERROR: crypt() returned null with 4-line file

2017-09-12 Thread Sean T. Ma

Hi FS experts,

I ran into a crypt() error while running the `recon-all` on a test brain
with Freesurfer 6.0 installed. The server is an FIPS enabled RHEL7.

In the `recon-all.log`, the error happened after the `mri_convert.bin`
execution: ERROR: crypt() returned null with 4-line file

I have attached a snippet below as well as the recon-all.log.

Has anyone encountered this error before? I'm suspecting the issue might be
due to the enabling of FIPS on RHEL7. I'm having similar OpenSSL prolembs
in FSL/FSLeyes.

Your input is appreciated!


Best,

Sean


mri_convert /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii
/nfs/fmri/Analysis/FSresults/test/mri/orig/001.mgz

mri_convert.bin /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii
/nfs/fmri/Analysis/FSresults/test/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii...
ERROR: crypt() returned null with 4-line file
Linux madcbrain.umms.med.umich.edu 3.10.0-693.el7.x86_64 #1 SMP Thu Jul 6
19:56:57 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s test exited with ERRORS at Wed Sep  6 12:01:48 EDT 2017


recon-all.log
Description: Binary data
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[Freesurfer] Course in Advanced Neuroimaging (Barcelona)

2017-09-12 Thread Erick Canales

Dear colleagues,

I am pleased to announce our upcoming Course in Advanced Neuroimaging held
annually in Barcelona. It takes a practical approach and does not require
qualifications or previous experience in neuroimaging. It will be taught in
Spanish.

The multidisciplinary programme provides thorough training in the analysis
of brain images from different MRI modalities and data modeling techniques,
including voxel-based morphometry, cortical thickness, diffusion tensor
imaging, fibre tracking, functional MRI and brain connectivity, as well as
the statistical methods behind these techniques including elements of
meta-analysis, and more.

The course consists of a five-month online theoretical module (starting on
November 6th) and a period of practical face-to-face training (split
between two days in November and two weeks at the end of April) held in
Barcelona.

For further information, please visit the website: www.cursoneuroimagen.com

Best regards,

Erick J. Canales-Rodríguez
Joaquim Radua
Raymond Salvador
Edith Pomarol-Clotet
FIDMAG Research Foundation and Sociedad Española de Neuroimagen
*www.fidmag.com *
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[Freesurfer] QDEC FDR for left and right hemispheres

2017-09-12 Thread Huang, Caleb (NIH/NINDS) [F]

Hello,


When I run FDR on QDEC, I get different p-values for the left and right 
hemispheres. Is it appropriate to use just one threshold for the sake of 
consistency?


Also, as an unrelated question, is there a way to display the thresholds as 
p-values rather than log(p)?


-Caleb
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[Freesurfer] PetSurfer GTM: gtmstats2table

2017-09-12 Thread Elijah Mak

Hi Doug,

Would it be possible to use the gtmstats2table command to extract GTM values 
from other parellations?

Thanks!

Best Wishes,
Elijah


Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge,
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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Re: [Freesurfer] do I need to re-ROI the segmentation after recon-all

2017-09-12 Thread Bruce Fischl


Hi Lawrence

yes, you should look through the data and make sure the results are 
reasonable. As for how much and where, that depends on what you are 
planning to do with it.


cheers
Bruce
On Tue, 12 Sep 2017, shi yao wang wrote:


Dear FS experts: 
After I finishing recon-all, do I need to check the segmentation and re-roi 
some of region?
thanks
Lawrence

Emory University



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Re: [Freesurfer] (no subject)

2017-09-12 Thread Bruce Fischl


Hi Yvonne

can you try using freeview instead? We don't really support tksurfer any 
longer.


cheers
Bruce
On Tue, 12 Sep 2017, y...@nyu.edu wrote:



Hi all,

 

I have finished the command “recon -all” without error. But I get an error that 
says:

“Received X error!

  Error code :158

  Request code : 148

  Minor code: 2

  Error text :’GLXBadLargeRequest’”

 

I am using the command “tksurfer sub lh inflated”.

Then clicking the File->Label->load label.->

and choosing document of “the lh.apare.a2009.annot”.

 

 

I don’t know why I got this error so would you be able to explain why this is 
the case and how I can
go about resolving this problem?

 

Best,

Yvonne

 


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Re: [Freesurfer] labels used by freesurfer

2017-09-12 Thread Benjamin Luerweg

dear mr. Greve,
dear fs community,

first of all thank you very much for helping me so far.

what i don’t understand is the difference between the value CSF (within the 
aseg.stat) and the CSFVol which shows up inside 
the console while processing the command to generate the aseg.stat file.

additional to this i would like to know why some of this values directly 
showing up inside the console are not included/part of the final aseg.stat?!
is there a different way to get a file which includes this morphometric data? 
(because like i told you: for example the aseg.stat value CSF differs from the 
inside the console shown value CSFVol (which is not part of aseg))

regarding to this ratio which i need its the VBR i meant 
(https://en.wikipedia.org/wiki/Ventricular-brain_ratio 
)
whats the best way to calculate this value? which parameters should i use?

my last question is about how to calculate the whole corpus calosum volume - is 
it possible to add all CC values to a value for the complete CC?

thank your very much in advance,
benjamin luerweg

_

> Am 11.09.2017 um 22:01 schrieb Douglas N Greve :
> 
> 
> 
> On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
>> dear fs community,
>> 
>> as a kind of a freesurfer greenhorn i would kindly ask you to help me 
>> out with identifying the different labels used by freesurfer.
>> after using mri segstats most of the labels seem to be describing 
>> thereselfs in proper way.
>> 
>> what i don’t understand are for example the different volume values 
>> showing up inside the console after entering the segstat command.
>> 
>> VentChorVol what does this label explain?
> Volume of all ventricles plus the volume of the chorioid plexus.
>> 
>> CSFVolwhy is this volume differing to the one within the segstat file?
> Volume of all ventricles (not well named because it does not include 
> extra cerebral CSF)
>> 
>> and finally i would really love to know how to calculate a correct 
>> brain to liquor ratio?!
> Do you mean brain volume to total CSF volume? See above
>> 
>> 
>> kind regards,
>> ben
>> 
>> 
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> MGH-NMR Center
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[Freesurfer] automatic quality control in freesurfer

2017-09-12 Thread shi yao wang

Dear FS experts:
Just wondering if there were any automatic method to perform quality
control especially for segmentation.

thanks
Lawrence
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[Freesurfer] do I need to re-ROI the segmentation after recon-all

2017-09-12 Thread shi yao wang

Dear FS experts:
After I finishing recon-all, do I need to check the segmentation and re-roi
some of region?

thanks
Lawrence

Emory University
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[Freesurfer] Results display tool

2017-09-12 Thread Chris Adamson

Freesurfer users,

I just wanted to advertise a set of display tools that I wrote for easy 
display, in MATLAB, of regional stats like p-values/effect sizes/arbitrary 
scalars with customisable masks for aparc, dkt, aparc.a2009s.

https://chrisadamsonmcri.github.io/freesurfer_statsurf_display

I hope people find it useful.

Chris.

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Re: [Freesurfer] side effects launching recon-all from matlab system(cmd) call

2017-09-12 Thread Giuseppe Cabras

Thanks Douglas for your reply.

I checked in detail the talairach_avi.log files and they show that
imgreg_4dfp c executable:

$Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $

are executed in both environment (bash and matlab), but in bash
imgreg_4dfp call in turn

$Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $

that show eta,q values in the talairach_avi.log file. Seems to me that,
if I call recon-all from matlab, fimgreg code ( which I don't know where
it is) is not executed or it don't write results to talairach_avi.log
output, but probably talairach avi transform is fine.

... very strange behaviour.

Cheers,

Giuseppe

On 11/09/2017 18:25, Douglas N Greve wrote:

The tal_QC_AZS scripts expects the log file to have a specific format,
and it looks like something changes when you run it inside matlab.
sorry, the only idea I have is that the linux environments might be
different in bash vs matlab.

On 09/11/2017 08:25 AM, Giuseppe Cabras wrote:

Dear freesurfer developers,

I call recon-all -all from a matlab script using a system(cmd) which
is (apparently) correctly executed, as shown in the recon-all.log
(matlab_* attached), i.e.:

/usr/local/freesurfer/bin/recon-all
-all -cw256 -3T -multistrip -clean-bm -i
/home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s
/home/gc/study/recon-all/400614dclass

and apparently it run without errors as you can see in the
matlab_recon-all.log file, but I get (systematically) a wrong

TalAviQA: 0.0

while, if I run the above bash command directly I get a correct:

TalAviQA: 0.97713

as shown in the bash_recon-all.log (attached). I guessed that
something wrong happened in

talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
--atlas 3T18yoSchwartzReactN32_as_orig

and the error traced in talairach_avi.log (matlab_* and bash_*
attached). In fact matlab_talairach_avi.log is shorter and all
imgreg_4dfp end sections are missing which imply that TalAviQA can not
be extracted by awk and mritotal transform is performed instead. But
really I don't understand why this happens and whether similar issues
affects other recon-all subtask using matlab. I double checked this on
two linux sistems and with fs version 6.0 and 5.3 ... same results.

Thanks in advance for any help,

cheers,

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University of Udine - via delle Scienze, 206 - 33100 UDINE
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Et sunt qui scire volunt, ut sciantur ipsi; et turpis vanitas est. [...]
Et sunt item qui scire volunt ut scientiam suam vendant; verbi causa, pro
pecunia,
pro honoribus: et turpis quaestus est. Sed sunt quoque qui scire volunt, ut
aedificent;
et charitas est. Et item qui scire volunt, ut aedificentur: et prudentia est.
Horum omnium soli ultimi duo non inveniuntur in abusione scientiae,
quippe qui ad hoc volunt intelligere ut bene faciant.
Denique: Intellectus bonus omnibus facientibus eum.
Reliqui omnes audiant: Scienti bonum et non facienti, peccatum est ei.
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Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

2017-09-12 Thread M Janani

Hi Douglas,

We tried running this command. But command not found error.

Thanks,
Janani




-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 12 September 2017 01:25
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

Try running

unsetenv FS_LOAD_DWI


then re-running recon-all

On 09/11/2017 12:57 PM, M Janani wrote:
>
> Hi Team,
>
> Am getting segmentation error during the 
> reconstruction process.
>
> Please help in resolving the error.
>
> I have attached log for reference.
>
> Thanks,
>
> Janani
>
>
>
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Re: [Freesurfer] Results display tool

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[Freesurfer] Resampling Freesurfer - Human connectome workbench

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Re: [Freesurfer] Q re: cluster commands

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Re: [Freesurfer] lobes volume (WM and GM)

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Re: [Freesurfer] QDEC FDR for left and right hemispheres

Re: [Freesurfer] PetSurfer GTM: gtmstats2table

Re: [Freesurfer] labels used by freesurfer

Re: [Freesurfer] side effects launching recon-all from matlab system(cmd) call

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

[Freesurfer] FS6.0 on RHEL7 FIPS enabled - ERROR: crypt() returned null with 4-line file

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[Freesurfer] QDEC FDR for left and right hemispheres

[Freesurfer] PetSurfer GTM: gtmstats2table

Re: [Freesurfer] do I need to re-ROI the segmentation after recon-all

Re: [Freesurfer] (no subject)

Re: [Freesurfer] labels used by freesurfer

[Freesurfer] automatic quality control in freesurfer

[Freesurfer] do I need to re-ROI the segmentation after recon-all

[Freesurfer] Results display tool

Re: [Freesurfer] side effects launching recon-all from matlab system(cmd) call

Re: [Freesurfer] mri_convert: line 3: 38445 Segmentation fault

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