[Freesurfer] Cortical Segmentation reliability in Mid-Line structures

[amirhossein manzouri]

Dear All,
I wonder if you have experienced or there is any report on cortical
segmentation reliability in the mid-line structures of the brain, so one
should take them into consideration in running group differences with Qdec?

Best regards,
Amirhossein Manzouri
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Re: [Freesurfer] Cortical Segmentation reliability in Mid-Line structures

[Bruce Fischl]

Hi Amirhossein

which structures do you mean? Like the ventricles? We usually mask those 
regions out using the ?h.cortex.label. The surfaces should be "frozen" in 
those regions in any case, meaning that the white and pial are in the same 
location (and the thickness is 0)


cheers
Bruce



On Mon, 11 Aug 2014, amirhossein 
manzouri wrote:



Dear All, 
I wonder if you have experienced or there is any report on cortical 
segmentation reliability in the
mid-line structures of the brain, so one should take them into consideration in 
running group differences
with Qdec?

Best regards,
Amirhossein Manzouri 

 


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[Freesurfer] dt_recon error

[Ritobrato Datta]

Hi All,

I ran dt_recon and got the following error. Can someone suggest how to fix this 
? I have attached the dwi-infodump.dat file for more information. 

Thanks a lot for the help.

Best

Rito

#@#---
Fitting Tensors
Mon Aug 11 07:29:29 EDT 2014
cd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003
mri_glmfit --y 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii 
--glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003
cmdline mri_glmfit --y 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii 
--glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon --dti 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
 
sysname  Darwin
hostname magi-2-balthasar.uphs.upenn.edu
machine  x86_64
user iron
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii
logyflag 1
X
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
usedti  1
glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon
Loading y from 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii
Using DTI
bValue = 1000
ERROR: cannot extract sWiPMemBlock.alFree[8] from 
/Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat

dwi-infodump.dat
Description: Binary data
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[Freesurfer] Any good cortical segmentation methods for brains with infarct or tumors?

[Salil Soman]

Hi,

Does anyone have recommendations for good automated cortical segmentation
tools for brains with infarct (so some brain missing) or tumors? I am under
the impression that FreeSurfer is not reliable in these cases. If I am
incorrect, any pointers on how to use  FreeSurfer in these cases would be
very helpful.

Thank you.

Salil

Thanks
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Re: [Freesurfer] lobes gyrification

[melinda dora]

hi thank you marie. Ive tried this but it doesnt give me one single spreadsheet 
for the value of each subjects lgi, just produces a file in each subjects stats 
directory. How do I make a spreadsheet with everybody's lgi values in it?

Kind Wishes, 

Melly

From: marie.sch...@unige.ch
To: freesurfer@nmr.mgh.harvard.edu; mellyd...@outlook.com
Subject: Re: [Freesurfer] lobes gyrification
Date: Mon, 21 Jul 2014 18:36:23 +










Hi Melly,



The LGI has the same format as the thickness files, so you can extract them 
using mris_anatomical_stats (providing you have your own annotation). The 
command will look something like:



mris_anatomical_stats -a $SUBJ/label/YOUR_ANNOT  -t $SUBJ/surf/?h.pial_lgi  -f 
$SUBJ/stats/OUTPUT_FILE  $SUBJ  ?h



Hope it helps,



Marie






On Jul 19, 2014, at 7:29 AM, melinda dora  wrote:



Dear freesurfer group, is there a command to extract lobar gyrification values 
for each subject? If so please what are the steps? if Ive already created the 
lobar annotation labels, can I extract gyrifaction with these if I have already 
passed
 the gyrification command?



Best,



Melly


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Re: [Freesurfer] lobes gyrification

[Marie Schaer]

Hi Melly,

You can use aparcstats2table from the file you created:

aparcstats2table --subjects  ….  --hemi lh --meas thickness --parc aparc_lgi 
--t summary_lgi.txt

Here you'll read the column "thickness" in the lh.aparc_lgi.stats file that you 
have created with mri_anatomical_stats (i.e. corresponding to lGI in this case, 
and not thickness). The name of the file can change, but has to start with ?h. 
for the hemi, and ends with .stats

Best,

Marie



On Aug 11, 2014, at 3:31 PM, melinda dora 
mailto:mellyd...@outlook.com>> wrote:

hi thank you marie. Ive tried this but it doesnt give me one single spreadsheet 
for the value of each subjects lgi, just produces a file in each subjects stats 
directory. How do I make a spreadsheet with everybody's lgi values in it?

Kind Wishes,

Melly


From: marie.sch...@unige.ch
To: freesurfer@nmr.mgh.harvard.edu; 
mellyd...@outlook.com
Subject: Re: [Freesurfer] lobes gyrification
Date: Mon, 21 Jul 2014 18:36:23 +


Hi Melly,

The LGI has the same format as the thickness files, so you can extract them 
using mris_anatomical_stats (providing you have your own annotation). The 
command will look something like:

mris_anatomical_stats -a $SUBJ/label/YOUR_ANNOT  -t $SUBJ/surf/?h.pial_lgi  -f 
$SUBJ/stats/OUTPUT_FILE  $SUBJ  ?h

Hope it helps,

Marie


On Jul 19, 2014, at 7:29 AM, melinda dora 
mailto:mellyd...@outlook.com>> wrote:

Dear freesurfer group, is there a command to extract lobar gyrification values 
for each subject? If so please what are the steps? if Ive already created the 
lobar annotation labels, can I extract gyrifaction with these if I have already 
passed the gyrification command?

Best,

Melly
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[Freesurfer] midline cortical thickness

[Ivanka Savic Berglund]

Question regarding reliability of midline cortical regions by Amir - it refers 
to the cingulate cortex, the cuneus, precuneus. 
Sincerely
Ivanka Savic M.D., PhD
> Professor of Neurology
> Karolinska Institute
> Dept of Women’s and Children’s Health
> and Neurology Clinic,Karolinska Hospital, Q2:07
> SE-171 76  STOCKHOLM, Sweden
> 
> Telephone +46 8 517 773 41
> +46 709 38 07 38 
> Fax+46 8 517 773 49
> ivanka.savic-bergl...@ki.se


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Re: [Freesurfer] dt_recon error

[Lilla Zollei]

Hi Rito.

It is not finding information about the gradient table that was used for 
the acquisition. If you have that information you can use the below option 
to manually include it

--b bvals bvecs

If you do not you could try using load_dicom in order to grab that 
information.

Lilla

On Mon, 11 Aug 2014, Ritobrato Datta wrote:

> Hi All,
>
> I ran dt_recon and got the following error. Can someone suggest how to fix 
> this ? I have attached the dwi-infodump.dat file for more information.
>
> Thanks a lot for the help.
>
> Best
>
> Rito
>
> #@#---
> Fitting Tensors
> Mon Aug 11 07:29:29 EDT 2014
> cd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003
> mri_glmfit --y 
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii 
> --glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon 
> --dti 
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
>
> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
> cwd /Users/iron/rito/VisualMeasures-CHOP/VisionMeasures-003
> cmdline mri_glmfit --y 
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii 
> --glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon 
> --dti 
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
> sysname  Darwin
> hostname magi-2-balthasar.uphs.upenn.edu
> machine  x86_64
> user iron
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii
> logyflag 1
> X
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
> usedti  1
> glmdir /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory 
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon
> Loading y from 
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-ec.nii
> Using DTI
> bValue = 1000
> ERROR: cannot extract sWiPMemBlock.alFree[8] from 
> /Applications/freesurfer5.1/subjects/VisionMeasures-003/dtrecon/dwi-infodump.dat
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[Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

[krista kelly]

Just wanted to pose this question again to the Freesurfer community:

Can anyone provide any advice on how to justify using the V1, V2 labels in
FreeSurfer in clinical populations without also collecting functional
retinotopy data?

Thanks!
Krista

-- Forwarded message --
From: krista kelly 
Date: Wed, Jun 18, 2014 at 4:51 PM
Subject: Re: [Freesurfer] V1 and V2 labels valid with clinical populations?
To: Freesurfer support list 


OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how to justify using these labels in clinical populations without
also collecting functional retinotopy data?


On Wed, Jun 18, 2014 at 4:13 PM, Bruce Fischl 
wrote:

> Hi Krista
>
> I don't think we have any idea. The labels are based purely on anatomy, but
> whether those areas keep their functional specification we have no idea.
>
> let us know if you find out though!
> Bruce
> On Wed, 18 Jun 2014, krista kelly wrote:
>
> > Does anyone know of any support (i.e. articles/data) suggesting that the
> V1
> > and V2 labels automatically created in the Freesurfer pipeline,
> especially
> > when looking at surface area/gyrification, are valid to use with clinical
> > populations? In particular, visually deprived populations?
> > Thanks!
> > Krista
> >
> >
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>
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Re: [Freesurfer] mri_em_register intervention?

[Bruce Fischl]

It looks more likely that it is a problem with the skull stripping. If you 
clone the brain voxels back in and rerun do things work?

> On Aug 11, 2014, at 4:11 PM, "Makaretz, Sara Johanna" 
>  wrote:
> 
> I am having trouble getting a usable brainmask for one of my subjects -
> a screenshot of the initial brainmask.mgz is attached as image_1. The
> talairach transformation looks fine, so I tried running recon-all
> -multistrip with raised watershed heights to no avail - see image_2.
> 
> Does this mean the problem is with the mri_em_register step / lta
> output? How can I check this, and what can I try changing?
> 
> Thank you!
> 
> 
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Re: [Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

[Ritobrato Datta]

Hi Krista,

Please refer to the following publications from Geoff Aguirre's lab -

http://www.ncbi.nlm.nih.gov/pubmed/23041195

http://www.ncbi.nlm.nih.gov/pubmed/24676149

All templates are in fsaverage_sym space in .mgh format and are available for 
download

https://cfn.upenn.edu/aguirre/wiki/public:data_currbio_2012_benson

https://cfn.upenn.edu/aguirre/wiki/public:data_ploscomputbiol_2014_benson

Best

Rito

- Original Message -
From: krista kelly 
To: freesurfer 
Sent: Mon, 11 Aug 2014 11:45:17 -0400 (EDT)
Subject: [Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

Just wanted to pose this question again to the Freesurfer community:

Can anyone provide any advice on how to justify using the V1, V2 labels in
FreeSurfer in clinical populations without also collecting functional
retinotopy data?

Thanks!
Krista

-- Forwarded message --
From: krista kelly 
Date: Wed, Jun 18, 2014 at 4:51 PM
Subject: Re: [Freesurfer] V1 and V2 labels valid with clinical populations?
To: Freesurfer support list 


OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how to justify using these labels in clinical populations without
also collecting functional retinotopy data?


On Wed, Jun 18, 2014 at 4:13 PM, Bruce Fischl 
wrote:

> Hi Krista
>
> I don't think we have any idea. The labels are based purely on anatomy, but
> whether those areas keep their functional specification we have no idea.
>
> let us know if you find out though!
> Bruce
> On Wed, 18 Jun 2014, krista kelly wrote:
>
> > Does anyone know of any support (i.e. articles/data) suggesting that the
> V1
> > and V2 labels automatically created in the Freesurfer pipeline,
> especially
> > when looking at surface area/gyrification, are valid to use with clinical
> > populations? In particular, visually deprived populations?
> > Thanks!
> > Krista
> >
> >
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>
>
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> 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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> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] error loading subjects in QDEC

[Nick Schmansky, MGH]

Katie,

Hi, is the SUBJECTS_DIR set to the proper directory?  I see from the
output that it is set to:

SUBJECTS_DIR is
'/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3'

which seems to imply that it might be set to the location of your
freesurfer installation, and not the location of the subject data (the
directory where '1009', '1014', etc. are found).

N.



On Tue, 2014-08-05 at 23:07 +, McLaughlin, Katie wrote:
> Hi Nick et al,
> 
> Just wanted to follow up on this.  It seems as though Nick Schmansky has 
> worked through this issue with previous FS users who have had the same error.
> 
> We are having an issue with QDEC recognizing subjects in the SUBJECTS_DIR.  
> It is not a permissions issue (777 for all) and all the subjects are in the 
> directory following recon-all and the qcache completed.  The data table loads 
> but cannot find any of the subjects.  Data table was created in Linux.
> 
> Nick - we have searched through the archives and haven't found a solution to 
> this issue, although a number of other users have had the same problem.  I'm 
> wondering if you've found a solution?
> 
> Many thanks,
> Kate
> 
> Error Output:
> 
> Reading 
> /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/tktools/tkUtils.tcl
> 
> Using 
> /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/lib/tcl/fsgdfPlot.tcl
> 
> Loading data table 
> /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat...
> Number of columns:  8
> fsid column:1
> Number of factors:  7
> Number of subjects: 42
> 
> Data table 
> /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat
>  loaded.
> Verifying subject data.sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in 
> SUBJECTS_DIR
> .sh: 1: Syntax error: Bad fd number
> ERROR:

Re: [Freesurfer] error loading subjects in QDEC

[McLaughlin, Katie]

Hi Nick,

Thanks for responding.  We found a solution to the issue with the SUBJECTS_DIR 
(which was pointing to the location of our data, not the FS installation).  
This issue appeared after doing some software updates on our cluster (including 
Ubuntu).  Here is how we fixed it:

sudo mv /bin/sh /bin/sh.orig
sudo ln -s /bin/bash /bin/sh

However, once we got that issue fixed, we've been having another issue that we 
haven't been able to resolve.  I would love any thoughts you have.  The data 
table loads successfully, it reads in the correct number of discrete and 
continuous factors and can find all the subjects.  However, when we go to 
analyze the data, we get an error in the terminal that says:  ERROR: 
QdecGlmDesign::Create: zero factors!

I can't find any information about this in the archive and am stumped as to 
what is going on.  Do you have any thoughts?

Many thanks!
Kate

Full output here:

Loading data table 
/neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat...
Number of columns:  8
fsid column:1
Number of factors:  7
Number of subjects: 42

Data table 
/neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat
 loaded.
Verifying subject data..Subject 
verification complete.
Input table: 
/neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat
Subj#, SubjID, Data...
1 1009 0.00 0.763636 0.00 0.00 1.50 -3.547619 348130.00 
2 1014 0.00 0.098336 0.00 0.00 -11.50 -10.547619 
149370.00 
3 1032 0.00 2.507636 0.00 0.00 2.50 0.452381 -960.00 
4 1034 0.00 0.101136 0.00 0.00 -15.50 -11.547619 
190570.00 
5 1041 1.00 -2.516264 0.00 1.00 17.50 12.452381 
-26620.00 
6 1043 1.00 -1.453964 0.00 0.00 7.50 12.452381 
205250.00 
7 1047 0.00 -0.933764 0.00 0.00 -10.50 -0.547619 
-73620.00 
8 1058 1.00 1.171636 1.00 0.00 14.50 7.452381 -42730.00 
9 1077 0.00 0.281836 1.00 0.00 -16.50 -12.547619 
-40610.00 
   10 1094 1.00 0.142136 1.00 0.00 3.50 -1.547619 
-158930.00 
   11 1096 0.00 -1.711364 1.00 0.00 -6.50 -6.547619 
31690.00 
   12 1097 0.00 -0.323264 1.00 0.00 6.50 0.452381 
-218300.00 
   13 1099 0.00 2.488536 0.00 0.00 -14.50 -8.547619 
279160.00 
   14 1100 1.00 1.404336 1.00 0.00 9.50 -0.547619 -77570.00 
   15 1114 1.00 -0.312264 1.00 0.00 -10.50 -12.547619 
141560.00 
   16 1119 1.00 -1.374564 0.00 0.00 -7.50 18.452381 
110660.00 
   17 1123 1.00 0.988136 0.00 0.00 33.50 16.452381 
-27400.00 
   18 1125 0.00 0.287236 1.00 0.00 -7.50 -8.547619 
-67320.00 
   19 1126 0.00 -1.820864 0.00 0.00 -14.50 -12.547619 
348770.00 
   20 1128 0.00 -1.338964 1.00 0.00 -0.50 -6.547619 
-101590.00 
   21 1134 0.00 -2.086464 1.00 0.00 -4.50 -5.547619 
-42360.00 
   22 1137 1.00 1.324936 0.00 0.00 12.50 23.452381 
-108080.00 
   23 1139 1.00 0.875936 1.00 0.00 -4.50 0.452381 
-199980.00 
   24 1142 1.00 -0.851664 1.00 0.00 10.50 2.452381 
-386850.00 
   25 1143 1.00 -2.820164 1.00 0.00 11.50 -13.547619 
-109600.00 
   26 1153 1.00 -2.458764 1.00 0.00 13.50 10.452381 
369170.00 
   27 1154 1.00 -1.234964 1.00 0.00 -8.50 -2.547619 
-261410.00 
   28 1157 0.00 1.034736 1.00 1.00 -10.50 -6.547619 
-67330.00 
   29 1158 1.00 1.163436 1.00 0.00 11.50 11.452381 
-71900.00 
   30 1163 1.00 1.371436 0.00 0.00 15.50 7.452381 239550.00 
   31 1165 1.00 -0.517664 0.00 1.00 -11.50 -2.547619 
16810.00 
   32 1166 1.00 -2.302764 0.00 1.00 -7.50 1.452381 
220140.00 
   33 1167 1.00 0.292736 1.00 1.00 12.50 11.452381 
-117810.00 
   34 1171 0.00 1.385136 1.00 0.00 6.50 -7.547619 59040.00 
   35 1173 0.00 1.075736 1.00 0.00 -7.50 2.452381 -86380.00 
   36 1175 0.00 1.765736 1.00 0.00 -1.50 -6.547619 
-31300.00 
   37 1176 0.00 1.732836 0.00 0.00 -11.50 -3.547619 
108560.00 
   38 1177 1.00 0.717136 1.00 0.00 -5.50 10.452381 
-53070.00 
   39 1178 1.00 -0.241164 1.00 0.00 33.50 15.452381 
-110020.00 
   40 1179 0.00 0.944336 1.00 0.00 -7.50 0.452381 15300.00 
   41 1180 0.00 0.760936 1.00 0.00 -18.50 -13.547619 
-97800.00 
   42 1181 0.00 -0.380764 1.00 0.00 -9.50 -7.547619 
-60610.00 
1  maltreatment  continuous 0
2  age_demean  co

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Jiahe Zhang]

There's nothing even when the threshold is set to 0.

I just checked the preprocessing outputs. I can see normal-looking volumes
fmcpr.nii.gz
fmcpr.up.nii.gz
fmcpr.up.sm6.mni305.2mm.nii.gz

But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or
fmcpr.up.sm6.fsaverage.rh.nii.gz




On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve 
wrote:

>
> When you say that they are "empty" what do you mean? That there is
> nothing above threshold or that there is nothing regardless of how low
> the threshold is? See if you get something if you set the thresh close
> to 0. Does this happen in the volume and the surface? Have you checked
> the registration to assure that it is accurate?
>
> On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > Hi Doug,
> >
> > I was trying to run functional connectivity analysis following
> > instructions on the FreeSurferWiki
> > (
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> ).
> > I was able to successfully run the following commands (nothing errored
> > as far as I can tell) but the resulting partial correlation and
> > significance maps turned out to be empty. Could you take a look at the
> > commands and let me know if anything can be improved?
> >
> > 1. PREPROC
> > preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh
> > -mni305-2mm -fsd bold -per-run -stc up
> >
> > 2. SEED CONFIG
> > fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold
> > -mean -cfg mean.L_Posteriorcingulate.config
> >
> > 3. SEED TIMECOURSE
> > fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config
> >
> > (wm.dat and vcsf.dat were similarly created)
> >
> > 4. ANALYSIS CONFIG
> > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage
> > lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg
> > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold
> > -TR 5 -per-run -lpf .1
> >
> > 5. ANALYSIS
> > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001
> >
> > Thanks,
> > Jiahe
> >
> >
> > --
> > Jiahe Zhang
> > Ph.D. Student
> > Department of Psychology
> > Northeastern University
> > 617-373-4789
> >
> >
> > ___
> > 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.
>
>


-- 
Jiahe Zhang
Ph.D. Student
Department of Psychology
Northeastern University
617-373-4789
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Douglas N Greve]

did you check the registration?

On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> There's nothing even when the threshold is set to 0.
>
> I just checked the preprocessing outputs. I can see normal-looking 
> volumes
> fmcpr.nii.gz
> fmcpr.up.nii.gz
> fmcpr.up.sm6.mni305.2mm.nii.gz
>
> But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or 
> fmcpr.up.sm6.fsaverage.rh.nii.gz
>
>
>
>
> On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> When you say that they are "empty" what do you mean? That there is
> nothing above threshold or that there is nothing regardless of how low
> the threshold is? See if you get something if you set the thresh close
> to 0. Does this happen in the volume and the surface? Have you checked
> the registration to assure that it is accurate?
>
> On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > Hi Doug,
> >
> > I was trying to run functional connectivity analysis following
> > instructions on the FreeSurferWiki
> >
> 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough).
> > I was able to successfully run the following commands (nothing
> errored
> > as far as I can tell) but the resulting partial correlation and
> > significance maps turned out to be empty. Could you take a look
> at the
> > commands and let me know if anything can be improved?
> >
> > 1. PREPROC
> > preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh
> > -mni305-2mm -fsd bold -per-run -stc up
> >
> > 2. SEED CONFIG
> > fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold
> > -mean -cfg mean.L_Posteriorcingulate.config
> >
> > 3. SEED TIMECOURSE
> > fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config
> >
> > (wm.dat and vcsf.dat were similarly created)
> >
> > 4. ANALYSIS CONFIG
> > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage
> > lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg
> > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold
> > -TR 5 -per-run -lpf .1
> >
> > 5. ANALYSIS
> > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001
> >
> > Thanks,
> > Jiahe
> >
> >
> > --
> > Jiahe Zhang
> > Ph.D. Student
> > Department of Psychology
> > Northeastern University
> > 617-373-4789
> >
> >
> > ___
> > 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.
>
>
>
>
> -- 
> Jiahe Zhang
> Ph.D. Student
> Department of Psychology
> Northeastern University
> 617-373-4789
>
>
> ___
> 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

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Jiahe Zhang]

I'm not sure how to check the registration. I see a register.dof6.dat being
produced for each run but I can't tell if it contains the correct
parameters. How can I tell if the registration was accurate?


On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve 
wrote:

> did you check the registration?
>
> On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > There's nothing even when the threshold is set to 0.
> >
> > I just checked the preprocessing outputs. I can see normal-looking
> > volumes
> > fmcpr.nii.gz
> > fmcpr.up.nii.gz
> > fmcpr.up.sm6.mni305.2mm.nii.gz
> >
> > But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or
> > fmcpr.up.sm6.fsaverage.rh.nii.gz
> >
> >
> >
> >
> > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > When you say that they are "empty" what do you mean? That there is
> > nothing above threshold or that there is nothing regardless of how
> low
> > the threshold is? See if you get something if you set the thresh
> close
> > to 0. Does this happen in the volume and the surface? Have you
> checked
> > the registration to assure that it is accurate?
> >
> > On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > > Hi Doug,
> > >
> > > I was trying to run functional connectivity analysis following
> > > instructions on the FreeSurferWiki
> > >
> > (
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> ).
> > > I was able to successfully run the following commands (nothing
> > errored
> > > as far as I can tell) but the resulting partial correlation and
> > > significance maps turned out to be empty. Could you take a look
> > at the
> > > commands and let me know if anything can be improved?
> > >
> > > 1. PREPROC
> > > preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh
> > > -mni305-2mm -fsd bold -per-run -stc up
> > >
> > > 2. SEED CONFIG
> > > fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd
> bold
> > > -mean -cfg mean.L_Posteriorcingulate.config
> > >
> > > 3. SEED TIMECOURSE
> > > fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config
> > >
> > > (wm.dat and vcsf.dat were similarly created)
> > >
> > > 4. ANALYSIS CONFIG
> > > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface
> fsaverage
> > > lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg
> > > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd
> bold
> > > -TR 5 -per-run -lpf .1
> > >
> > > 5. ANALYSIS
> > > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001
> > >
> > > Thanks,
> > > Jiahe
> > >
> > >
> > > --
> > > Jiahe Zhang
> > > Ph.D. Student
> > > Department of Psychology
> > > Northeastern University
> > > 617-373-4789
> > >
> > >
> > > ___
> > > 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  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.
> >
> >
> >
> >
> > --
> > Jiahe Zhang
> > Ph.D. Student
> > Department of Psychology
> > Northeastern University
> > 617-373-4789
> >
> >
> > ___
> > 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: 617-726-74

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Douglas N Greve]

two ways:

1. run tkregister-sess to visually check them
2. look at the first value in register.dof6.dat.mincost. It is hard to 
say what a threshold is for a good registration, but typical values are 
about .5 or so. If it is .8 or more, it is probably a problem (and 
probably the initialization is not good)


On 08/11/2014 04:35 PM, Jiahe Zhang wrote:
> I'm not sure how to check the registration. I see a register.dof6.dat 
> being produced for each run but I can't tell if it contains the 
> correct parameters. How can I tell if the registration was accurate?
>
>
> On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> did you check the registration?
>
> On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > There's nothing even when the threshold is set to 0.
> >
> > I just checked the preprocessing outputs. I can see normal-looking
> > volumes
> > fmcpr.nii.gz
> > fmcpr.up.nii.gz
> > fmcpr.up.sm6.mni305.2mm.nii.gz
> >
> > But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or
> > fmcpr.up.sm6.fsaverage.rh.nii.gz
> >
> >
> >
> >
> > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > When you say that they are "empty" what do you mean? That
> there is
> > nothing above threshold or that there is nothing regardless
> of how low
> > the threshold is? See if you get something if you set the
> thresh close
> > to 0. Does this happen in the volume and the surface? Have
> you checked
> > the registration to assure that it is accurate?
> >
> > On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > > Hi Doug,
> > >
> > > I was trying to run functional connectivity analysis following
> > > instructions on the FreeSurferWiki
> > >
> >
> 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough).
> > > I was able to successfully run the following commands (nothing
> > errored
> > > as far as I can tell) but the resulting partial
> correlation and
> > > significance maps turned out to be empty. Could you take a
> look
> > at the
> > > commands and let me know if anything can be improved?
> > >
> > > 1. PREPROC
> > > preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh
> > > -mni305-2mm -fsd bold -per-run -stc up
> > >
> > > 2. SEED CONFIG
> > > fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat
> -fsd bold
> > > -mean -cfg mean.L_Posteriorcingulate.config
> > >
> > > 3. SEED TIMECOURSE
> > > fcseed-sess -s subject_001 -cfg
> mean.L_Posteriorcingulate.config
> > >
> > > (wm.dat and vcsf.dat were similarly created)
> > >
> > > 4. ANALYSIS CONFIG
> > > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface
> fsaverage
> > > lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1
> -nuisreg
> > > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4
> -fsd bold
> > > -TR 5 -per-run -lpf .1
> > >
> > > 5. ANALYSIS
> > > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001
> > >
> > > Thanks,
> > > Jiahe
> > >
> > >
> > > --
> > > Jiahe Zhang
> > > Ph.D. Student
> > > Department of Psychology
> > > Northeastern University
> > > 617-373-4789
> > >
> > >
> > > ___
> > > 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/

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Jiahe Zhang]

Both looked fine. First value in .mincost is .45


On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve 
wrote:

> two ways:
>
> 1. run tkregister-sess to visually check them
> 2. look at the first value in register.dof6.dat.mincost. It is hard to
> say what a threshold is for a good registration, but typical values are
> about .5 or so. If it is .8 or more, it is probably a problem (and
> probably the initialization is not good)
>
>
> On 08/11/2014 04:35 PM, Jiahe Zhang wrote:
> > I'm not sure how to check the registration. I see a register.dof6.dat
> > being produced for each run but I can't tell if it contains the
> > correct parameters. How can I tell if the registration was accurate?
> >
> >
> > On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > did you check the registration?
> >
> > On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > > There's nothing even when the threshold is set to 0.
> > >
> > > I just checked the preprocessing outputs. I can see normal-looking
> > > volumes
> > > fmcpr.nii.gz
> > > fmcpr.up.nii.gz
> > > fmcpr.up.sm6.mni305.2mm.nii.gz
> > >
> > > But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz
> or
> > > fmcpr.up.sm6.fsaverage.rh.nii.gz
> > >
> > >
> > >
> > >
> > > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > >
> > > When you say that they are "empty" what do you mean? That
> > there is
> > > nothing above threshold or that there is nothing regardless
> > of how low
> > > the threshold is? See if you get something if you set the
> > thresh close
> > > to 0. Does this happen in the volume and the surface? Have
> > you checked
> > > the registration to assure that it is accurate?
> > >
> > > On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > > > Hi Doug,
> > > >
> > > > I was trying to run functional connectivity analysis
> following
> > > > instructions on the FreeSurferWiki
> > > >
> > >
> > (
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> ).
> > > > I was able to successfully run the following commands
> (nothing
> > > errored
> > > > as far as I can tell) but the resulting partial
> > correlation and
> > > > significance maps turned out to be empty. Could you take a
> > look
> > > at the
> > > > commands and let me know if anything can be improved?
> > > >
> > > > 1. PREPROC
> > > > preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh
> > > > -mni305-2mm -fsd bold -per-run -stc up
> > > >
> > > > 2. SEED CONFIG
> > > > fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat
> > -fsd bold
> > > > -mean -cfg mean.L_Posteriorcingulate.config
> > > >
> > > > 3. SEED TIMECOURSE
> > > > fcseed-sess -s subject_001 -cfg
> > mean.L_Posteriorcingulate.config
> > > >
> > > > (wm.dat and vcsf.dat were similarly created)
> > > >
> > > > 4. ANALYSIS CONFIG
> > > > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface
> > fsaverage
> > > > lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1
> > -nuisreg
> > > > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4
> > -fsd bold
> > > > -TR 5 -per-run -lpf .1
> > > >
> > > > 5. ANALYSIS
> > > > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s
> subject_001
> > > >
> > > > Thanks,
> > > > Jiahe
> > > >
> > > >
> > > > --
> > > > Jiahe Zhang
> > > > Ph.D. Student
> > > > Department of Psychology
> > > > Northeastern University
> > > > 617-373-4789
> > > >
> > > >
> > > > ___
> > > > 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
> > 
> > > 

Re: [Freesurfer] FsFast Functional Connectivity Analysis

[Douglas N Greve]

How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did not do 
this, try it

tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t 
fmcpr.up.sm6.fsaverage.lh.nii.gz

This will bring up an overlay as well as a time course


On 08/11/2014 05:05 PM, Jiahe Zhang wrote:
> Both looked fine. First value in .mincost is .45
>
>
> On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> two ways:
>
> 1. run tkregister-sess to visually check them
> 2. look at the first value in register.dof6.dat.mincost. It is hard to
> say what a threshold is for a good registration, but typical
> values are
> about .5 or so. If it is .8 or more, it is probably a problem (and
> probably the initialization is not good)
>
>
> On 08/11/2014 04:35 PM, Jiahe Zhang wrote:
> > I'm not sure how to check the registration. I see a
> register.dof6.dat
> > being produced for each run but I can't tell if it contains the
> > correct parameters. How can I tell if the registration was accurate?
> >
> >
> > On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> > did you check the registration?
> >
> > On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > > There's nothing even when the threshold is set to 0.
> > >
> > > I just checked the preprocessing outputs. I can see
> normal-looking
> > > volumes
> > > fmcpr.nii.gz
> > > fmcpr.up.nii.gz
> > > fmcpr.up.sm6.mni305.2mm.nii.gz
> > >
> > > But there is nothing when I open
> fmcpr.up.sm6.fsaverage.lh.nii.gz or
> > > fmcpr.up.sm6.fsaverage.rh.nii.gz
> > >
> > >
> > >
> > >
> > > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > >  
> >
> >  
> >   > >
> > >
> > > When you say that they are "empty" what do you mean? That
> > there is
> > > nothing above threshold or that there is nothing
> regardless
> > of how low
> > > the threshold is? See if you get something if you set the
> > thresh close
> > > to 0. Does this happen in the volume and the surface? Have
> > you checked
> > > the registration to assure that it is accurate?
> > >
> > > On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > > > Hi Doug,
> > > >
> > > > I was trying to run functional connectivity analysis
> following
> > > > instructions on the FreeSurferWiki
> > > >
> > >
> >
> 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough).
> > > > I was able to successfully run the following
> commands (nothing
> > > errored
> > > > as far as I can tell) but the resulting partial
> > correlation and
> > > > significance maps turned out to be empty. Could you
> take a
> > look
> > > at the
> > > > commands and let me know if anything can be improved?
> > > >
> > > > 1. PREPROC
> > > > preproc-sess -s subject_001 -fwhm 6 -surface
> fsaverage lhrh
> > > > -mni305-2mm -fsd bold -per-run -stc up
> > > >
> > > > 2. SEED CONFIG
> > > > fcseed-config -segid 1010 -fcname
> L_Posteriorcingulate.dat
> > -fsd bold
> > > > -mean -cfg mean.L_Posteriorcingulate.config
> > > >
> > > > 3. SEED TIMECOURSE
> > > > fcseed-sess -s subject_001 -cfg
> > mean.L_Posteriorcingulate.config
> > > >
> > > > (wm.dat and vcsf.dat were similarly created)
> > > >
> > > > 4. ANALYSIS CONFIG
> > > > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf
> -surface
> > fsaverage
> > > > lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1
> > -nuisreg
> > > > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5
> -nskip 4
> > -fsd bold
> > > > -TR 5 -per-run -lpf .1
> > > >
> > > > 5. ANALYSIS
> > > > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s
> subject_001
> > > >
> > > > Thanks,
> > > > Jiahe
> > > >
> > > >
> > > > --
> > > > Jiahe Zhang
> > > 

Re: [Freesurfer] error loading subjects in QDEC

[McLaughlin, Katie]

Hi Nick,

We solved this.

Thanks for your help,
Kate

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie 
[katie.mclaugh...@childrens.harvard.edu]
Sent: Monday, August 11, 2014 3:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] error loading subjects in QDEC

Hi Nick,

Thanks for responding.  We found a solution to the issue with the SUBJECTS_DIR 
(which was pointing to the location of our data, not the FS installation).  
This issue appeared after doing some software updates on our cluster (including 
Ubuntu).  Here is how we fixed it:

sudo mv /bin/sh /bin/sh.orig
sudo ln -s /bin/bash /bin/sh

However, once we got that issue fixed, we've been having another issue that we 
haven't been able to resolve.  I would love any thoughts you have.  The data 
table loads successfully, it reads in the correct number of discrete and 
continuous factors and can find all the subjects.  However, when we go to 
analyze the data, we get an error in the terminal that says:  ERROR: 
QdecGlmDesign::Create: zero factors!

I can't find any information about this in the archive and am stumped as to 
what is going on.  Do you have any thoughts?

Many thanks!
Kate

Full output here:

Loading data table 
/neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat...
Number of columns:  8
fsid column:1
Number of factors:  7
Number of subjects: 42

Data table 
/neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat
 loaded.
Verifying subject data..Subject 
verification complete.
Input table: 
/neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat
Subj#, SubjID, Data...
1 1009 0.00 0.763636 0.00 0.00 1.50 -3.547619 348130.00
2 1014 0.00 0.098336 0.00 0.00 -11.50 -10.547619 
149370.00
3 1032 0.00 2.507636 0.00 0.00 2.50 0.452381 -960.00
4 1034 0.00 0.101136 0.00 0.00 -15.50 -11.547619 
190570.00
5 1041 1.00 -2.516264 0.00 1.00 17.50 12.452381 
-26620.00
6 1043 1.00 -1.453964 0.00 0.00 7.50 12.452381 205250.00
7 1047 0.00 -0.933764 0.00 0.00 -10.50 -0.547619 
-73620.00
8 1058 1.00 1.171636 1.00 0.00 14.50 7.452381 -42730.00
9 1077 0.00 0.281836 1.00 0.00 -16.50 -12.547619 
-40610.00
   10 1094 1.00 0.142136 1.00 0.00 3.50 -1.547619 -158930.00
   11 1096 0.00 -1.711364 1.00 0.00 -6.50 -6.547619 31690.00
   12 1097 0.00 -0.323264 1.00 0.00 6.50 0.452381 -218300.00
   13 1099 0.00 2.488536 0.00 0.00 -14.50 -8.547619 
279160.00
   14 1100 1.00 1.404336 1.00 0.00 9.50 -0.547619 -77570.00
   15 1114 1.00 -0.312264 1.00 0.00 -10.50 -12.547619 
141560.00
   16 1119 1.00 -1.374564 0.00 0.00 -7.50 18.452381 
110660.00
   17 1123 1.00 0.988136 0.00 0.00 33.50 16.452381 -27400.00
   18 1125 0.00 0.287236 1.00 0.00 -7.50 -8.547619 -67320.00
   19 1126 0.00 -1.820864 0.00 0.00 -14.50 -12.547619 
348770.00
   20 1128 0.00 -1.338964 1.00 0.00 -0.50 -6.547619 
-101590.00
   21 1134 0.00 -2.086464 1.00 0.00 -4.50 -5.547619 
-42360.00
   22 1137 1.00 1.324936 0.00 0.00 12.50 23.452381 
-108080.00
   23 1139 1.00 0.875936 1.00 0.00 -4.50 0.452381 -199980.00
   24 1142 1.00 -0.851664 1.00 0.00 10.50 2.452381 
-386850.00
   25 1143 1.00 -2.820164 1.00 0.00 11.50 -13.547619 
-109600.00
   26 1153 1.00 -2.458764 1.00 0.00 13.50 10.452381 
369170.00
   27 1154 1.00 -1.234964 1.00 0.00 -8.50 -2.547619 
-261410.00
   28 1157 0.00 1.034736 1.00 1.00 -10.50 -6.547619 
-67330.00
   29 1158 1.00 1.163436 1.00 0.00 11.50 11.452381 -71900.00
   30 1163 1.00 1.371436 0.00 0.00 15.50 7.452381 239550.00
   31 1165 1.00 -0.517664 0.00 1.00 -11.50 -2.547619 
16810.00
   32 1166 1.00 -2.302764 0.00 1.00 -7.50 1.452381 220140.00
   33 1167 1.00 0.292736 1.00 1.00 12.50 11.452381 
-117810.00
   34 1171 0.00 1.385136 1.00 0.00 6.50 -7.547619 59040.00
   35 1173 0.00 1.075736 1.00 0.00 -7.50 2.452381 -86380.00
   36 1175 0.00 1.765736 1.00 0.00 -1.50 -6.547619 -31300.00
   37 1176 0.00 1.732836 0.00 0.00 -11.50 -3.547619 
108560.00
   38 1177 1.00 0.717136 1.00 0.00 -5.50 10.452381 -53070.00
   39 1178 1.00 -0.241164 1.00 0.00 33.

[Freesurfer] Mac OS X update

[carolina.mr]

Hi all,
 
I have a simple doubt: I am updating my MAC OS X from Snow Leopard to Mavericks.
 
I am worried if FreeSurfer is going to run perfectly in the new OS X?
 
Thank you, 
Carolina
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Re: [Freesurfer] -hippo-subfields

[Marcos Martins da Silva]

Hi, Greg
I use to process my subjects with:

recon-all -s subjid -all -hippo-subfields

The -all flag makes the program run all the 3 stages (autorecon1,
autorecon2 and autorecon3) in sequence. Only after this it starts the
hippo-subfields stage. If you do not have any special reason to run each
autorecon in a different line in your script I suggest you just use the
-all flag. But if you need to separate each stage you can use:

recon-all -s subjid -autorecon1
recon-all -s subjid -autorecon2
recon-all -s subjid -autorecon3 -hippo-subfields

No need to add the hippo-subfields flag for each stage: you would just
repeat the same process and waste time. Indeed, if you check
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation you 
will see that "...the program needs the FreeSurfer-generated files "aseg.mgz", 
"nu.mgz" and "talairach.xfm"
At least, aseg.mgz will not be available before completing autorecon2.
So I guess if you add the hippo-subfields flag after autorecon1 stage it
will return an error.
 
Marcos
Em Qui, 2014-08-07 às 16:05 -0500, Gregory Kirk escreveu:

> 
> we have freesurfer set up on our big condor cluster, i asked that the
> 
> -hippo-subfields be added. they have it set up to run in 3 stages
> autorecon1 autorecon2 autorecon3 
> they added the flag to all 3, i think it would only be needed on autorecon3, 
> but don't think it would
> cause harm, just be ignored in the first 2 ?
> 
> thanks
> 
> greg
> ___
> Freesurfer mailing list
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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] fsaverage cortex thickness

[wangzhiwei3233]

Hi, all,
How to calculate the mean cortex thickness of fsaverage?
Thanks!


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[Freesurfer] Flipped Hemisphere longitudinal analysis

[Bastian Cheng]

Dear Freesurfers,

Has anyone accomplished analysis of longitudinal cortex changes in a
dataset with "flipped" hemispheres?

I am currently struggling with data from stroke patients, half of them
with lesions on the right, half of them on the left side of the brain.

What I am planning: flip all healthy hemispheres to left and perform
longitud. analysis of cortical thickness change on that (helthy)
hemisphere.

I have read the notes on Surface-based Interhemispheric Registration
(xhemi) and most of the comments here. It seems to me that this would
allow me to compare both hemisph. sides at ONE timepoint. (but not
actually analyzing ONE (flipped) hemisphere over time).

Any help to point me in the right direction is greatly appreciated!

Bastian
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