[Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Jennifer Legault]

Hi Freesurfer Experts,

I am trying to run mri_glmfit and while 90% of my files work, some of them
display the error below.  I have tried demeaning, and then tried
multiplying this value by 100, and I still get the same error.  Any
feedback would be greatly appreciated.

mris_preproc done
srcsubject = fsaverage
srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
srctype=
trgsubject = fsaverage
trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= rh
trghemi= rh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
Reading source surface reg
/gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
Loading source data
INFO: trgsubject = srcsubject
Saving target data
Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
gdfReadHeader: reading
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 19.5833 1.32025
1 eTIV 1.61645e+06 145343
2 EnglishParityRT 0.00012207 25139.1
Class Means of each Continuous Variable
1 Monolingual_male  19.7143 1678946.5893 -4197.2796
2 Monolingual_female  19.4000 1528966.6750 5876.1917
INFO: gd2mtx_method is dods
Reading source surface
/gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces327680
Total area 65020.765625
AvgVtxArea   0.396850
AvgVtxDist   0.717994
StdVtxDist   0.193566

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /gpfs/scratch/jtl190/Math_reconstruction
cmdline mri_glmfit --y
rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
--C
/gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
--surf fsaverage rh --cortex --glmdir
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
sysname  Linux
hostname cyberstar129.hpc.rcc.psu.edu
machine  x86_64
user jtl190
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
 
/gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
logyflag 0
usedti  0
FSGD
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
labelmask
 /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
Loading y from
/gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
INFO: gd2mtx_method is dods
Saving design matrix to
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat
Normalized matrix condition is 22568.9
Design matrix --
 1.000   0.000   18.000   0.000   1865790.250   0.000  -8952.208   0.000;
 0.000   1.000   0.000   19.000   0.000   1520429.625   0.000  -4605.208;
 1.000   0.000   19.000   0.000   1749716.750   0.000  -39407.207   0.000;
 0.000   1.000   0.000   18.000   0.000   1589109.250   0.000  -17967.209;
 1.000   0.000   21.000   0.000   1472295.125   0.000   19531.791   0.000;
 1.000   0.000   18.000   0.000   1580381.375   0.000  -17027.209   0.000;
 1.000   0.000   20.000   0.000   1813373.500   0.000   16152.792   0.000;
 1.000   0.000   21.000   0.000   1638616.500   0.000  -9074.208   0.000;
 0.000   1.000   0.000   21.000   0.000   1297920.500   0.000   61860.793;
 0.000   1.000   0.000   18.000   0.000   1634762.625   0.000  -22671.209;
 0.000   1.000   0.000   21.000   0.000   1602611.375   0.000   12763.792;
 1.000   0.000   21.000   0.000   1632452.625   0.000   9395.292   0.000;

ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9

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 --y rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
--fsgd
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
--C
/gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
--surf fsaverage rh --cortex --glmdir
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above


I am also attaching the FSGD file.

Best,

Jennifer Legault


fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
Description: Binary data
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[Freesurfer] tcsh update

[shi yao wang]

Dear FS experts:
I am running FS in local computer and showing following error message and
program stopped at recon-all

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Do I need to update tcsh? and how can I do it.

thanks
Lawrence
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Re: [Freesurfer] V3A ROI?

[Bruce Fischl]

Hi Anders

thanks. Seems like you can just get the data from them and are all set.


Bruce

On Mon, 11 Jul 2016, Anders Hougaard wrote:


Excellent, thank you.The link to the ROI files is this:
http://www.princeton.edu/~napl/vtpm.htm

Best,
Anders

2016-07-11 12:26 GMT+02:00 Francesca Strappini
:
  Wang, Mruczek, Arcaro, Kastner (2014). 
  Probabilistic Maps of Visual Topography in Human Cortex.
  Cerebral Cortex, Oct;25(10):3911-31 


2016-07-11 12:13 GMT+02:00 Anders Hougaard :
  Dear experts,
I am trying to find a probabilistic map of the visual cortical
area V3A. 
I have not been able to find this particular area in the
standard atlases in FSL or FreeSurfer. The Jülich Histological
atlas contains a V3V ROI but not V3A.
Do any of you know have this ROI as a file or do you know of an
atlas which contains it?
An estimation based on an experiment, e.g. an average from
retinotopic maps of healthy subjects would also be very helpful.

All the best,
Anders


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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il

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Re: [Freesurfer] longitudinal qdec tables

[Martin Reuter]

So you exported CSV from excel on Mac with space separation and it does not work?
Try to export only a few lines to make sure it is not a weird character somewhere else. 
Best Martin
On Jul 11, 2016 5:44 PM, "Andrews, Derek"  wrote:





Hi Martin,


Thank you for the tip. Indeed there is some issue with the character spacing in my qdec file. 


I usually generate subject text files like this in excel and save them as csv .txt files. Do you have any suggestions for easily writing the qdec file without going line by line, space by space?


Best, Derek 








Derek
 Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental
 Sciences 

Institute of Psychiatry, Psychology
 & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk 








From: Martin Reuter 
Reply-To: Freesurfer support list 
Date: Mon, 11 Jul 2016 13:59:53 +0200
To: Freesurfer support list 
Subject: Re: [Freesurfer] longitudinal qdec tables



Hi Derek,
For debugging try a simple file with two lines (header and first row). Separate columns only with a space. Once that works add more rows.
Best Martin
On Jul 11, 2016 12:58 PM, "Andrews, Derek"  wrote:




Dear FreeSurfer Developers and Community,


I have been trying to run some commands using the —qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the —fsgd flag but am unsure of how to go about this with longitudinal
 data, therefore I am using the qdec.dat file structure.


I believe something must be wrong with the format of my qdec file. I’m working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See
 these qdec files attached. 


I receive the following errors:




asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

    subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs

    for row in reader:

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next

    self.fieldnames

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames

    self._fieldnames = self.reader.next()



_csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode?




And




mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh

ERROR: no subjects specified



I imagine something silly with the qdec file must be going on. Any advice would be very appreciated.


Best, Derek 





Derek
 Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental
 Sciences 

Institute of Psychiatry, Psychology
 & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk 








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Re: [Freesurfer] longitudinal qdec tables

[Andrews, Derek]

Hi Martin,

Thank you for the tip. Indeed there is some issue with the character spacing in 
my qdec file.

I usually generate subject text files like this in excel and save them as csv 
.txt files. Do you have any suggestions for easily writing the qdec file 
without going line by line, space by space?

Best, Derek




Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk


From: Martin Reuter 
>
Reply-To: Freesurfer support list 
>
Date: Mon, 11 Jul 2016 13:59:53 +0200
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] longitudinal qdec tables


Hi Derek,
For debugging try a simple file with two lines (header and first row). Separate 
columns only with a space. Once that works add more rows.

Best Martin

On Jul 11, 2016 12:58 PM, "Andrews, Derek" 
> wrote:
Dear FreeSurfer Developers and Community,

I have been trying to run some commands using the -qdec-long flag (I.e. 
asegstats2table & mris_preproc) but am encountering errors. In the past I have 
used .rtf files to read in my data using the -fsgd flag but am unsure of how to 
go about this with longitudinal data, therefore I am using the qdec.dat file 
structure.

I believe something must be wrong with the format of my qdec file. I'm working 
on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to 
.dat under get info (1). I also created one in gedit and saved it using a .dat 
suffix (2). See these qdec files attached.

I receive the following errors:


asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in 
assemble_inputs

for row in reader:

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 103, in next

self.fieldnames

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 90, in fieldnames

self._fieldnames = self.reader.next()

_csv.Error: new-line character seen in unquoted field - do you need to open the 
file in universal-newline mode?

And


mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh 
--meas thickness --out lh.thickness.mgh

ERROR: no subjects specified

I imagine something silly with the qdec file must be going on. Any advice would 
be very appreciated.

Best, Derek



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk

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[Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

[Knut J Bjuland]

 flirt.fsl 
-ref/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii-in/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii-bins
 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90-searchrz -90 90 
-verbose 0 
-omat/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat-init/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat-schedule
 /usr/local/freesurfer/bin/flirt.newdefault.20080811.schterminate called after 
throwing an instance of'NEWMAT::SingularException'Abort (core dumped) ERROR: 
flirtFedora 
24glibc-2.23.1-8.fc24.x86_64gcc-6.1.1-3.fc24.x86_64libstdc++-6.1.1-3.fc24.x86_64ldd
 /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000)   
 libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000)libstdc++.so.6 => 
/lib64/libstdc++.so.6(0x7feaeb67e000)libm.so.6 => /lib64/libm.so.6 
(0x7feaeb374000)libgcc_s.so.1 => /lib64/libgcc_s.so.1 
(0x7feaeb15d000)libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000)
/lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)Knut Jørgen Bjuland 
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Re: [Freesurfer] V3A ROI?

[Anders Hougaard]

Excellent, thank you.
The link to the ROI files is this:
http://www.princeton.edu/~napl/vtpm.htm

Best,
Anders

2016-07-11 12:26 GMT+02:00 Francesca Strappini :

> Wang, Mruczek, Arcaro, Kastner (2014).
> Probabilistic Maps of Visual Topography in Human Cortex.
> Cerebral Cortex, Oct;25(10):3911-31
>
>
> 2016-07-11 12:13 GMT+02:00 Anders Hougaard :
>
>> Dear experts,
>>
>> I am trying to find a probabilistic map of the visual cortical area V3A.
>> I have not been able to find this particular area in the standard atlases
>> in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but
>> not V3A.
>> Do any of you know have this ROI as a file or do you know of an atlas
>> which contains it?
>> An estimation based on an experiment, e.g. an average from retinotopic
>> maps of healthy subjects would also be very helpful.
>>
>> All the best,
>> Anders
>>
>>
>> ___
>> 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.
>>
>>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il
>
> ___
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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] mri_glmfit-sim

[Lauri Tuominen]

Dear Freesurfers,
As freesurfer mri_glmfit-sim is based on AlphaSim & FSL randomise, I would like 
to know if the results I’m getting are affected by recently found 
bugs/violations in RFT assumptions, e.g. 
http://www.pnas.org/content/early/2016/06/27/1602413113.full.pdf.

Thank you in advance!
Lauri Tuominen


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Re: [Freesurfer] V3A ROI?

[Bruce Fischl]

no, sorry, we don't have that data. If you ask the authors for it we 
would be happy to distribute it with FS if they are willing.


cheers
Bruce
On Mon, 11 Jul 
2016, Francesca Strappini wrote:



Wang, Mruczek, Arcaro, Kastner (2014). 
Probabilistic Maps of Visual Topography in Human Cortex.
Cerebral Cortex, Oct;25(10):3911-31 


2016-07-11 12:13 GMT+02:00 Anders Hougaard :
  Dear experts,
I am trying to find a probabilistic map of the visual cortical area
V3A. 
I have not been able to find this particular area in the standard
atlases in FSL or FreeSurfer. The Jülich Histological atlas contains a
V3V ROI but not V3A.
Do any of you know have this ROI as a file or do you know of an atlas
which contains it?
An estimation based on an experiment, e.g. an average from retinotopic
maps of healthy subjects would also be very helpful.

All the best,
Anders


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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il

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Re: [Freesurfer] right hemisphere specific problem with converting labels from fsaverage to subject space

[Bruce Fischl]

sorry, forgot to respond earlier. Which V1 label are you using? You might 
try thresholding it to remove the low-probability vertices that make it 
larger than it should be


cheers
Bruce
On Mon, 11 Jul 2016, Halbertsma, HN (ohk) wrote:



I’m having issues with the conversion of labels drawn in fsaverage to
subject’s space (using mri_label2label). 
I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left
and right hemisphere that I want to convert to a subjects brain. I’ve
successfully managed to do this for the left hemisphere of all the subjects,
where the V1-bins converted from the fsaverage fall perfectly within subject
specific V1. However, for the right hemisphere, the bins seem slightly
misaligned for all the subjects (they’re usually a bit bigger than they
should be). Any idea what could have caused this?! 

Attached the image that shows the fine conversion for the lh (on the left)
and the misaligned conversion for the rh (on the right)

[IMAGE]

I used the following commands:

left hemisphere, first bin: 
mri_label2label --srcsubject fsaverage --srclabel
./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel
./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod surface

right hemisphere
mri_label2label --srcsubject fsaverage --srclabel
./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel
./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod surface

The output is as follows:
left hemisphere, first bin:
srclabel = ./fsaverage/label/lh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = HHcon_8
trglabel = ./HHcon_8/label/lh.v1_nbin1_from_fsaverage
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 102 points in source label.
Starting surface-based mapping
Reading source registration 
 /Applications/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /Applications/freesurfer/subjects/HHcon_8/surf/lh.white
Reading target registration 
 /Applications/freesurfer/subjects/HHcon_8/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  102 nlabel points
Performing mapping from target back to the source label 118606
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./HHcon_8/label/lh.v1_nbin1_from_fsaverage 132
mri_label2label: Done

right hemisphere, first bin:
srclabel = ./fsaverage/label/rh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = con21_oxford
trglabel = ./con21_oxford/label/rh.v1_nbin1_from_fsaverage
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 209 points in source label.
Starting surface-based mapping
Reading source registration 
 /Applications/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /Applications/freesurfer/subjects/con21_oxford/surf/rh.white
Reading target registration 
 /Applications/freesurfer/subjects/con21_oxford/surf/rh.sphere.reg
Rescaling ...  original radius = 99.
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  209 nlabel points
Performing mapping from target back to the source label 145838
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./con21_oxford/label/rh.v1_nbin1_from_fsaverage 294
mri_label2label: Done

So for some reason the conversion for the right hemisphere works but is not
perfect, which is also reflected in the fact that extracting the label
statistics (using mris_anatomical_stats) will sometimes give different
values after re-running the conversion.


Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl







  On 01 Jul 2016, at 16:11, Halbertsma, HN (ohk)
   wrote:

Hi Bruce,

Attached the image that show the fine conversion for the lh (on the
left) and the misaligned conversion for the rh (on the right)



I used the following commands:

left hemisphere, first bin: 
mri_label2label --srcsubject fsaverage --srclabel
./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel
./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod
surface

right hemisphere
mri_label2label --srcsubject fsaverage --srclabel

Re: [Freesurfer] longitudinal qdec tables

[Martin Reuter]

Hi Derek,
For debugging try a simple file with two lines (header and first row). Separate columns only with a space. Once that works add more rows.
Best Martin
On Jul 11, 2016 12:58 PM, "Andrews, Derek"  wrote:






Dear FreeSurfer Developers and Community,


I have been trying to run some commands using the —qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the —fsgd flag but am unsure of how to go about this with longitudinal
 data, therefore I am using the qdec.dat file structure.


I believe something must be wrong with the format of my qdec file. I’m working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See
 these qdec files attached. 


I receive the following errors:




asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

    subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs

    for row in reader:

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next

    self.fieldnames

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames

    self._fieldnames = self.reader.next()



_csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode?




And




mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh

ERROR: no subjects specified



I imagine something silly with the qdec file must be going on. Any advice would be very appreciated.


Best, Derek 





Derek
 Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental
 Sciences 

Institute of Psychiatry, Psychology
 & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk 







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[Freesurfer] longitudinal qdec tables

[Andrews, Derek]

Dear FreeSurfer Developers and Community,

I have been trying to run some commands using the -qdec-long flag (I.e. 
asegstats2table & mris_preproc) but am encountering errors. In the past I have 
used .rtf files to read in my data using the -fsgd flag but am unsure of how to 
go about this with longitudinal data, therefore I am using the qdec.dat file 
structure.

I believe something must be wrong with the format of my qdec file. I'm working 
on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to 
.dat under get info (1). I also created one in gedit and saved it using a .dat 
suffix (2). See these qdec files attached.

I receive the following errors:


asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in 
assemble_inputs

for row in reader:

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 103, in next

self.fieldnames

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 90, in fieldnames

self._fieldnames = self.reader.next()

_csv.Error: new-line character seen in unquoted field - do you need to open the 
file in universal-newline mode?

And


mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh 
--meas thickness --out lh.thickness.mgh

ERROR: no subjects specified

I imagine something silly with the qdec file must be going on. Any advice would 
be very appreciated.

Best, Derek



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk



1.long.qdec.table.dat
Description: 1.long.qdec.table.dat


2.long.qdec.table.dat
Description: 2.long.qdec.table.dat
fsidfsid-base   years
0008Y1  00080
0011Y1  00110
0011Y2  00110.490410959
0012Y1  00120
0012Y2  00120.490410959
0033Y1  00330
0033Y2  00330
0093Y1  00930
0095Y1  00950
0095Y2  00950.95890411
0097Y2  00970
0098Y1  00980
0101Y1  01010
0101Y2  01010.989041096
0101Y3  01011.980821918
0104Y1  01040
0105Y3  01050
0106Y1  01060
0106Y2  01061.208219178
0107Y3  01070
0108Y2  01080
0110Y1  01100
0110Y3  01102.169863014
0112Y1  01120
0112Y2  01121.054794521
0114Y1  01140
0114Y2  01141.315068493
0116Y1  01160
0116Y2  01160.989041096
0117Y1  01170
0120Y1  01200
0127Y1  01270
0128Y1  01280
0134Y1  01340
0135Y1  01350
0135Y2  01350
0136Y1  01360
0136Y2  01361.002739726
0136Y3  01362
0137Y3  01370
0138Y1  01380
0139Y1  01390
0139Y3  01390.978082192
0146Y3  01460
0153Y1  01530
0153Y2  01530.95890411
0153Y3  01531.994520548
0158Y1  01580
0158Y2  01581.169863014
0160Y2  01600
0160Y3  01601.035616438
0175Y1  01750
0175Y2  01750
0180Y1  01800
1004Y2  10040
1005Y1  10050
1005Y2  10051.178082192
1005Y3  10052.301369863
1006Y2  10060
1006Y3  10060.997260274
1007Y1  10070
1009Y1  10090
1016Y2  10160
1017Y1  10170
1017Y2  10171.054794521
1017Y3  10172.123287671
1022Y1  10220
1023Y1  10230
1023Y2  10231.476712329
1027Y1  10270
1027Y2  10270.961643836
1032Y2  10320
1032Y3  10321.054794521
1034Y1  10340
1034Y2  10341.112328767
1034Y3  10342.109589041
1041Y1  10410
1041Y3  10412.293150685
1042Y2  10420
1042Y3  10420.997260274
1044Y1  10440
1045Y2  10450
1046Y1  10460
1046Y2  10461.109589041
1046Y3  10462.068493151
1052Y1  10520
1052Y2  10521.156164384
1052Y3  10522.271232877
1054Y2  10540
1054Y3  10541.073972603
1057Y2  10570
1057Y3  10570.912328767
1071Y2  10710
1071Y3  10710
1073Y3  10730
1075Y2  10750
1075Y3  10750.978082192
1077Y1  10770
1091Y1  10910
1091Y2  10910
1091Y3  10911.994520548
1096Y2  10960
Y1  0
Y3  2.473972603
1121Y1  11210
1121Y2  11211.22739726
1141Y1  11410
1144Y3  11440
1151Y1  11510
1159Y1  11590
1159Y2  11590.989041096
1159Y3  11592.024657534
1161Y1  11610
1161Y2  1161-0.115068493
1164Y1  11640
1164Y2  11641.035616438___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you 

Re: [Freesurfer] V3A ROI?

[Francesca Strappini]

Wang, Mruczek, Arcaro, Kastner (2014).
Probabilistic Maps of Visual Topography in Human Cortex.
Cerebral Cortex, Oct;25(10):3911-31


2016-07-11 12:13 GMT+02:00 Anders Hougaard :

> Dear experts,
>
> I am trying to find a probabilistic map of the visual cortical area V3A.
> I have not been able to find this particular area in the standard atlases
> in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but
> not V3A.
> Do any of you know have this ROI as a file or do you know of an atlas
> which contains it?
> An estimation based on an experiment, e.g. an average from retinotopic
> maps of healthy subjects would also be very helpful.
>
> All the best,
> Anders
>
>
> ___
> 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.
>
>


-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] right hemisphere specific problem with converting labels from fsaverage to subject space

[Halbertsma, HN (ohk)]

I’m having issues with the conversion of labels drawn in fsaverage to subject’s 
space (using mri_label2label).
I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left 
and right hemisphere that I want to convert to a subjects brain. I’ve 
successfully managed to do this for the left hemisphere of all the subjects, 
where the V1-bins converted from the fsaverage fall perfectly within subject 
specific V1. However, for the right hemisphere, the bins seem slightly 
misaligned for all the subjects (they’re usually a bit bigger than they should 
be). Any idea what could have caused this?!

Attached the image that shows the fine conversion for the lh (on the left) and 
the misaligned conversion for the rh (on the right)

[cid:9B79D24B-8ECE-46FA-889C-B7919A94C7B2]

I used the following commands:

left hemisphere, first bin:
mri_label2label --srcsubject fsaverage --srclabel 
./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel 
./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod surface

right hemisphere
mri_label2label --srcsubject fsaverage --srclabel 
./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel 
./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod surface

The output is as follows:
left hemisphere, first bin:
srclabel = ./fsaverage/label/lh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = HHcon_8
trglabel = ./HHcon_8/label/lh.v1_nbin1_from_fsaverage
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 102 points in source label.
Starting surface-based mapping
Reading source registration
 /Applications/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
 /Applications/freesurfer/subjects/HHcon_8/surf/lh.white
Reading target registration
 /Applications/freesurfer/subjects/HHcon_8/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  102 nlabel points
Performing mapping from target back to the source label 118606
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./HHcon_8/label/lh.v1_nbin1_from_fsaverage 132
mri_label2label: Done

right hemisphere, first bin:
srclabel = ./fsaverage/label/rh.v1_nbin1.label
srcsubject = fsaverage
trgsubject = con21_oxford
trglabel = ./con21_oxford/label/rh.v1_nbin1_from_fsaverage
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Loading source label.
Found 209 points in source label.
Starting surface-based mapping
Reading source registration
 /Applications/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface
 /Applications/freesurfer/subjects/con21_oxford/surf/rh.white
Reading target registration
 /Applications/freesurfer/subjects/con21_oxford/surf/rh.sphere.reg
Rescaling ...  original radius = 99.
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  209 nlabel points
Performing mapping from target back to the source label 145838
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./con21_oxford/label/rh.v1_nbin1_from_fsaverage 294
mri_label2label: Done

So for some reason the conversion for the right hemisphere works but is not 
perfect, which is also reflected in the fact that extracting the label 
statistics (using mris_anatomical_stats) will sometimes give different values 
after re-running the conversion.


Hinke N. Halbertsma, MSc

PhD Student
University Medical Center Groningen (UMCG)
Department of Ophthalmology
NeuroImaging Center (Antonius Deusinglaan 2,  9713 AW Groningen), room 124
T. (+31) 050 363 4431
E. h.n.halbert...@umcg.nl







On 01 Jul 2016, at 16:11, Halbertsma, HN (ohk) 
> wrote:

Hi Bruce,

Attached the image that show the fine conversion for the lh (on the left) and 
the misaligned conversion for the rh (on the right)



I used the following commands:

left hemisphere, first bin:
mri_label2label --srcsubject fsaverage --srclabel 
./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel 
./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod surface

right hemisphere
mri_label2label --srcsubject fsaverage --srclabel 
./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel 
./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod surface

The 

[Freesurfer] V3A ROI?

[Anders Hougaard]

Dear experts,

I am trying to find a probabilistic map of the visual cortical area V3A.
I have not been able to find this particular area in the standard atlases
in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but
not V3A.
Do any of you know have this ROI as a file or do you know of an atlas which
contains it?
An estimation based on an experiment, e.g. an average from retinotopic maps
of healthy subjects would also be very helpful.

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

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi Anastasia,
There is an error in .log files of left corticospinal tract in cvs template
and I attached one of file. In addition .log files of right corticospinal
tract in cvs template doesn't exist.
Thanks in advance.

Anri



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

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - Is there an error in the stats/*.log files for the different
> tracts?
>
> a.y
>
>
> On Tue, 5 Jul 2016, Anri WATANABE wrote:
>
> Dear Anastasia,
>>
>> I use TRACULA to obtain diffusion measures at each voxel in a certain
>> pathway for group analysis, but
>> there aren't stats/*.path.mean.txt files. I found .log files
>> (_PP.avg33_mni_bbr.log) which exist
>> 1 file per 1 tract, except corticospinal tract which has 2 .log files.
>>
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference volume from
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> I attached dmrirc.example (configuration file) and
>> /scripts/trac-all.log.
>>
>>
>> Thanks in advance,
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-06-03 9:51 GMT+09:00 Anri WATANABE :
>>   Hi, Anastasia.
>> There aren't any .log files but text files like
>> lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text
>> files complete all pathways and measures.
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-06-02 3:03 GMT+09:00 Anastasia Yendiki > >:
>>
>>   Thanks, Anri. So the previous steps seem to have run fine. Are
>> there any .log files
>>   created in the stats/ folder, which is created by trac-all -stat?
>>
>>   On Wed, 1 Jun 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia, This is a /scripts/trac-all.log of one
>> subject of
>> the group.
>>
>> Thanks,
>> Anri
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - Can you also send your log file
>> (scripts/trac-all.log)?
>> I'll need to see what
>>   exactly was running when the error occurred. Thanks!
>>
>>   a.y
>>
>>   On Sat, 28 May 2016, Anri WATANABE wrote:
>>
>> Hello Anastasia,sorry for few information and let
>> me tell you
>> command and
>> error log.
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference volume from
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>>
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> dmrirc.example (configuration file) is attached
>> to this
>> e-mail.
>>
>> Thanks in advance,
>> Anri
>>
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>>
>>