date:20160128

it's called mris_ca_label, and yes, that is what I mean. If you tell us 
your hardware/software environment Zeke can get you a binary


On Thu, 28 Jan 2016, 
Fengji Geng wrote:




Hi Bruce,

Did you mean an updated version of mri_parcellate? If so, it would be great.

Thanks!

 



 

 

Hi Fengji

 

this is a known bug in mris_parcellate. We can give you an updated version

if you want, but you should probably rerun all your subjects using it. The

good news is that it's fast - just a couple of min/hemi

 

cheers

Bruce

  On Tue, 26 Jan

2016, Fengji Geng wrote:

 

> Hello fs experts,

>

> We ran a command like ?recon-all -all -s HMN002
-hippocampal-subfields-T1T2

> HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)?

> (which is also attached below). The error log file is also attached here.?

>

> Error msg:

>---

> --

> setting seed for random number generator to 1234

> using ../mri/aseg.presurf.mgz aseg volume to correct midline

> $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $

> ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $

> reading 
atlasfrom/cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.f
ille

> d.desikan_killiany.2010-03-25.gcs...

> reading color table from GCSA file

> average std = 1.0?? using min determinant for regularization = 0.011

> 0 singular and 384 ill-conditioned covariance matrices regularized

> input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature

> labeling surface...

> 1592 labels changed using aseg

> relabeling using gibbs priors...

> 000:?? 2975 changed, 134786 examined...

> 001:??? 698 changed, 12707 examined...

> 002:??? 152 changed, 3873 examined...

> 003: 50 changed, 880 examined...

> 004: 29 changed, 284 examined...

> 005: 16 changed, 164 examined...

> 006:? 7 changed, 87 examined...

> 007:? 1 changed, 42 examined...

> 008:? 0 changed, 4 examined...

> 206 labels changed using aseg

> 000: 105 total segments, 64 labels (264 vertices) changed

> 001: 43 total segments, 4 labels (14 vertices) changed

> 002: 39 total segments, 0 labels (0 vertices) changed

> 1 filter iterations complete (10 requested, 0 changed)

> Abort (core dumped)

> Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23

> 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux

>

> recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016

>

> Our freesurfer information:

>  freesurfer-Linux-centos6_x86_64-dev-20151215 

> Setting up environment for FreeSurfer/FS-FAST (and FSL)

> FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys

> FSFAST_HOME?? /cell_root/software/freesurfer/dev/sys/fsfast

> FSF_OUTPUT_FORMAT nii.gz

> SUBJECTS_DIR? /export/data/hippocampus/HMN/data

> MNI_DIR?? /cell_root/software/freesurfer/dev/sys/mni

> FSL_DIR?? /cell_root/software/fsl/new/sys

>

> Looking forward to hearing how we can resolve this error. Also, thanks in

> advance.

>

> Best,

>

> - Fengji

>

>

> 

 

 

---

Fengji

 


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Re: [Freesurfer] Segmentation depends on image file format

2016-01-28 Thread Parzer, Peter

mri_convert

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von dgw 

Gesendet: Donnerstag, 28. Januar 2016 15:55
An: Freesurfer support list
Betreff: Re: [Freesurfer] Segmentation depends on image file format

What software did you use to generate the NIFTI files? Many of the
converters do different things to the axes of the data, and this does
affect results.

hth
d

On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter
 wrote:
> Hi,
>
> we have brain images stored as DICOM and as NIFTI files. For some time we 
> used to import the NIFTI files to freesurfer for segmentation. I was curious 
> if it makes a difference if we would import the DICOM files directly, and was 
> surprised that it actually did. Here are the commands we used:
>
> # Import DICOM files
> recon-all -s 3003PC_dcm -i 
> ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm
>
> # Convert DICOM to NIFTI and import NIFTI file
> mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm 
> 3003PC.nii.gz
> recon-all -s 3003PC_nii -i 3003PC.nii.gz
>
> # Segmentation of DICOM file import
> recon-all -s 3003PC_dcm -all
>
> # Segmentation of NIFTI file import
> recon-all -s 3003PC_nii -all
>
> Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import)
>
>   1   4  5612 5611.8  Left-Lateral-Ventricle27.6355
> 12.8465 8.93.85.
>   2   5   452  452.2  Left-Inf-Lat-Vent 42.1100
> 14.9377 7.86.79.
>   3   7 1376513765.1  Left-Cerebellum-White-Matter  87.7808 
> 6.600836.   109.73.
>
> and here the the first 3 volumes for 3003PC_nii (NIFTI import)
>
>   1   4  5582 5582.2  Left-Lateral-Ventricle27.4507
> 12.7212 8.93.85.
>   2   5   421  421.1  Left-Inf-Lat-Vent 40.8032
> 14.6554 7.83.76.
>   3   7 1389913898.6  Left-Cerebellum-White-Matter  87.6707 
> 6.753936.   109.73.
>
> The differences are small but I think there should be no differences at all. 
> Has someone an explanation for this differences and which file format is 
> better?
>
> Greetings
> Peter
>
> P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on 
> Ubuntu 14.04
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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 
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Re: [Freesurfer] Fwd: hardware question

How many cores/processors? In an earlier email you stated that you 
wanted to process many recons at the same time. If this is the case than 
the number of processors would be the limiting factor.

FYI: Freesurfer version 6 will include a "-parallel" flag which will use 
4 processors (by to default) to proces both the left and right 
hemispheres of the brain. This drastically reduces runtime and the 
expense of resources.

On 01/28/2016 04:26 AM, Joost Janssen wrote:
> Hi,
>
> We're thinking of buying a computer with the main goal simultaneous
> processing of 'recon-all's'. the computer cannot be a 'cluster' and must
> be linux. These specs looked good to us:
>
> - Intel Core i7-5820K 3.3Ghz
>
> - Asus X99-A
>
> - Arctic Cooling Freezer A30 CPU Cooler
>
> - G.Skill Aegis DDR4 2400 PC4-19200 16GB CL15
>
> - Samsung 850 Evo SSD Series 500GB SATA3
>
> - Toshiba 4TB 7200rpm SATA3
>
> - Aerocool Aero 800 Negra USB 3.0
>
> - AeroCool KCAS 700W 80 Plus Bronze
>
> - Asus GeForce Strix GTX 960 DirectCU II OC 4GB GDDR5
>
> Are there things we can improve at? Thanks for any advice!
> -joost
>
>
>
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Re: [Freesurfer] Segmentation depends on image file format

p.s or maybe on the 001.mgz in the mri/orig subdir as well
On Thu, 28 Jan 
2016, Parzer, Peter wrote:

> mri_convert
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von dgw 
> 
> Gesendet: Donnerstag, 28. Januar 2016 15:55
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Segmentation depends on image file format
>
> What software did you use to generate the NIFTI files? Many of the
> converters do different things to the axes of the data, and this does
> affect results.
>
> hth
> d
>
> On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter
>  wrote:
>> Hi,
>>
>> we have brain images stored as DICOM and as NIFTI files. For some time we 
>> used to import the NIFTI files to freesurfer for segmentation. I was curious 
>> if it makes a difference if we would import the DICOM files directly, and 
>> was surprised that it actually did. Here are the commands we used:
>>
>> # Import DICOM files
>> recon-all -s 3003PC_dcm -i 
>> ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm
>>
>> # Convert DICOM to NIFTI and import NIFTI file
>> mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm 
>> 3003PC.nii.gz
>> recon-all -s 3003PC_nii -i 3003PC.nii.gz
>>
>> # Segmentation of DICOM file import
>> recon-all -s 3003PC_dcm -all
>>
>> # Segmentation of NIFTI file import
>> recon-all -s 3003PC_nii -all
>>
>> Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import)
>>
>>   1   4  5612 5611.8  Left-Lateral-Ventricle27.6355
>> 12.8465 8.93.85.
>>   2   5   452  452.2  Left-Inf-Lat-Vent 42.1100
>> 14.9377 7.86.79.
>>   3   7 1376513765.1  Left-Cerebellum-White-Matter  87.7808 
>> 6.600836.   109.73.
>>
>> and here the the first 3 volumes for 3003PC_nii (NIFTI import)
>>
>>   1   4  5582 5582.2  Left-Lateral-Ventricle27.4507
>> 12.7212 8.93.85.
>>   2   5   421  421.1  Left-Inf-Lat-Vent 40.8032
>> 14.6554 7.83.76.
>>   3   7 1389913898.6  Left-Cerebellum-White-Matter  87.6707 
>> 6.753936.   109.73.
>>
>> The differences are small but I think there should be no differences at all. 
>> Has someone an explanation for this differences and which file format is 
>> better?
>>
>> Greetings
>> Peter
>>
>> P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on 
>> Ubuntu 14.04
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>
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>
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>
>
>
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Re: [Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05 {Disarmed}

Are there areas in the overlay that are positive and greater than 1.3 ? 
If so, they should show up in thresholded.mgh. If they are negative, 
then you'll need to use --max  -1.3  and leave --min unspecified 
(defaults to -infinity)

On 01/28/2016 05:01 AM, Erik Lindberg wrote:
> Dear Bruce and Freesufers,
>
>
> I get the following message:
>
>
> surfer: Interpreting overlay volume 
> /media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glmdir/Gend/thresholded.mgh
>  
> as encoded scalar volume.
>
>
> the two volumes I tried to convert:
>
> 1)
>
> Volume information for sig.mgh
> type: MGH
> dimensions: 163842 x 1 x 1
> voxel sizes: 1., 1., 1.
> type: FLOAT (3)
> fov: 163842.000
> dof: 0
> xstart: -81921.0, xend: 81921.0
> ystart: -0.5, yend: 0.5
> zstart: -0.5, zend: 0.5
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
> nframes: 1
> PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
> 0.
> : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
> : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
>
> talairach xfm :
> Orientation : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
> -1.   0.   0. 81921.
> 0.   0.   1.-0.5000
> 0.  -1.   0. 0.5000
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
> -1.   0.   0. 81921.
> -0.  -0.  -1. 0.5000
> -0.   1.  -0. 0.5000
> 0.   0.   0. 1.
>
>
> 2)
>
>
> Volume information for cache.th13.abs.sig.cluster.mgh
> type: MGH
> dimensions: 163842 x 1 x 1
> voxel sizes: 1., 1., 1.
> type: FLOAT (3)
> fov: 163842.000
> dof: 0
> xstart: -81921.0, xend: 81921.0
> ystart: -0.5, yend: 0.5
> zstart: -0.5, zend: 0.5
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
> nframes: 1
> PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
> 0.
> : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
> : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
>
> talairach xfm :
> Orientation : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
> -1.   0.   0. 81921.
> 0.   0.   1.-0.5000
> 0.  -1.   0. 0.5000
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
> -1.   0.   0. 81921.
> -0.  -0.  -1. 0.5000
> -0.   1.  -0. 0.5000
> 0.   0.   0. 1.
>
>
> Although both these overlays have significant areas - nothing appears 
> on the binarized version after the conversion
>
>
> Best wishes,
>
> Olof Lindberg
>
> Olof Lindberg PhD
> Novum plan 5
> NVS department section clinical geriatrics
> 14186 Stockholm
> +46722255711
> *MailScanner has detected a possible fraud attempt from "email.ki.se" 
> claiming to be* http://www.oloflindberg.se 
> 
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] fast_selxavg3 error when Octave is used

Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ?

On 01/28/2016 07:16 AM, m.abouelya...@gmail.com wrote:
>
> Since I am a windows user I got the Virtualbox version of FreeSurfer 
> and to use fs fast, I installed Octave on the virtual machine, I set 
> the environment variables and then when I run the command
>
> selxavg3-sess -analysis rtopy.lh -sf sessid
>
> which runs a retinotopy analysis, I get the following error:
>
> sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx
>
> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis 
> rtopy.lh -sf sessid
>
> error: `fast_fileexists' undefined near line 5 column 4
>
> --
>
> ERROR: fast_selxavg3() failed\n
>
> Any idea of the cause of this error and how to run around?
>
> Thank you,
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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[Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh

2016-01-28 Thread Erik Lindberg

Dear Bruce and Freesurfer,

Yes, that is what I am saying! This what appears in the commandprompt when
running the command:

input  cache.th13.abs.sig.cluster.mgh
frame  0
nErode3d   0
nErode2d   0
output thresholded.mgh
Binarizing based on threshold
min1.3
max+infinity
binval1
binvalnot 0
Found 12485 values in range
Counting number of voxels
Found 12485 voxels in final mask
mri_binarize done

Yet nothing is visible when I open the thresholded surface in tksurfer.


previous:

what was the command line and screen output of the binarization? And are
you saying that pre-binarization you have locations that are above
threshold, but they are set to 0 anyway?
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Re: [Freesurfer] Segmentation depends on image file format

can you run mri_diff on the orig.mgz in the two runs and send us the 
output?
On Thu, 28 Jan 2016, Parzer, Peter wrote:

> mri_convert
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von dgw 
> 
> Gesendet: Donnerstag, 28. Januar 2016 15:55
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Segmentation depends on image file format
>
> What software did you use to generate the NIFTI files? Many of the
> converters do different things to the axes of the data, and this does
> affect results.
>
> hth
> d
>
> On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter
>  wrote:
>> Hi,
>>
>> we have brain images stored as DICOM and as NIFTI files. For some time we 
>> used to import the NIFTI files to freesurfer for segmentation. I was curious 
>> if it makes a difference if we would import the DICOM files directly, and 
>> was surprised that it actually did. Here are the commands we used:
>>
>> # Import DICOM files
>> recon-all -s 3003PC_dcm -i 
>> ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm
>>
>> # Convert DICOM to NIFTI and import NIFTI file
>> mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm 
>> 3003PC.nii.gz
>> recon-all -s 3003PC_nii -i 3003PC.nii.gz
>>
>> # Segmentation of DICOM file import
>> recon-all -s 3003PC_dcm -all
>>
>> # Segmentation of NIFTI file import
>> recon-all -s 3003PC_nii -all
>>
>> Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import)
>>
>>   1   4  5612 5611.8  Left-Lateral-Ventricle27.6355
>> 12.8465 8.93.85.
>>   2   5   452  452.2  Left-Inf-Lat-Vent 42.1100
>> 14.9377 7.86.79.
>>   3   7 1376513765.1  Left-Cerebellum-White-Matter  87.7808 
>> 6.600836.   109.73.
>>
>> and here the the first 3 volumes for 3003PC_nii (NIFTI import)
>>
>>   1   4  5582 5582.2  Left-Lateral-Ventricle27.4507
>> 12.7212 8.93.85.
>>   2   5   421  421.1  Left-Inf-Lat-Vent 40.8032
>> 14.6554 7.83.76.
>>   3   7 1389913898.6  Left-Cerebellum-White-Matter  87.6707 
>> 6.753936.   109.73.
>>
>> The differences are small but I think there should be no differences at all. 
>> Has someone an explanation for this differences and which file format is 
>> better?
>>
>> Greetings
>> Peter
>>
>> P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on 
>> Ubuntu 14.04
>> ___
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
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>
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[Freesurfer] mris_preproc on zipped data

2016-01-28 Thread Lars M. Rimol

Hi,

I have a large amount of data (FS scanworkups) where all the files within
every subject's directory are zipped. Is there a way to run mris_preproc on
zipped data?

For instance, mris_preproc crashes because it can't find lh.thickness
unless I unzip it


Thank you!







sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
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Re: [Freesurfer] Segmentation depends on image file format

I suspect that it has to do with the image geometry information. In 
nifit, this is stored in quaterion format. In FS, this is converted to 
direction cosines. This conversion is not reversible. So when you 
mri_convert the DICOMS to nii, mri_convert will get the direction 
cosines from the dicom file and convert them to quaternions. When you 
run recon-all using the nii file, the quaternions are converted back to 
direction cosines. But this does not yield exactly the same as what was 
in the dicom file. This conversion does not happen when you start out 
with mgz files. In version 6 I changed the code to try to reduce this 
effect, but I think it will always be there.

On 01/28/2016 10:49 AM, Bruce Fischl wrote:
> can you run mri_diff on the orig.mgz in the two runs and send us the
> output?
> On Thu, 28 Jan 2016, Parzer, Peter wrote:
>
>> mri_convert
>> 
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  im Auftrag von dgw 
>> 
>> Gesendet: Donnerstag, 28. Januar 2016 15:55
>> An: Freesurfer support list
>> Betreff: Re: [Freesurfer] Segmentation depends on image file format
>>
>> What software did you use to generate the NIFTI files? Many of the
>> converters do different things to the axes of the data, and this does
>> affect results.
>>
>> hth
>> d
>>
>> On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter
>>  wrote:
>>> Hi,
>>>
>>> we have brain images stored as DICOM and as NIFTI files. For some time we 
>>> used to import the NIFTI files to freesurfer for segmentation. I was 
>>> curious if it makes a difference if we would import the DICOM files 
>>> directly, and was surprised that it actually did. Here are the commands we 
>>> used:
>>>
>>> # Import DICOM files
>>> recon-all -s 3003PC_dcm -i 
>>> ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm
>>>
>>> # Convert DICOM to NIFTI and import NIFTI file
>>> mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm 
>>> 3003PC.nii.gz
>>> recon-all -s 3003PC_nii -i 3003PC.nii.gz
>>>
>>> # Segmentation of DICOM file import
>>> recon-all -s 3003PC_dcm -all
>>>
>>> # Segmentation of NIFTI file import
>>> recon-all -s 3003PC_nii -all
>>>
>>> Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import)
>>>
>>>1   4  5612 5611.8  Left-Lateral-Ventricle27.6355
>>> 12.8465 8.93.85.
>>>2   5   452  452.2  Left-Inf-Lat-Vent 42.1100
>>> 14.9377 7.86.79.
>>>3   7 1376513765.1  Left-Cerebellum-White-Matter  87.7808
>>>  6.600836.   109.73.
>>>
>>> and here the the first 3 volumes for 3003PC_nii (NIFTI import)
>>>
>>>1   4  5582 5582.2  Left-Lateral-Ventricle27.4507
>>> 12.7212 8.93.85.
>>>2   5   421  421.1  Left-Inf-Lat-Vent 40.8032
>>> 14.6554 7.83.76.
>>>3   7 1389913898.6  Left-Cerebellum-White-Matter  87.6707
>>>  6.753936.   109.73.
>>>
>>> The differences are small but I think there should be no differences at 
>>> all. Has someone an explanation for this differences and which file format 
>>> is better?
>>>
>>> Greetings
>>> Peter
>>>
>>> P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on 
>>> Ubuntu 14.04
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>>> Freesurfer mailing list
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
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>>
>>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

[Freesurfer] FreeSurfer 6 Release Date & El Capitan SIP issues

2016-01-28 Thread Shady El Damaty

Hi,

I was curious to know what the tentative release date for FreeSurfer 6 is.  I’m 
currently running FreeSurfer on multiple machines with El Capitan installed and 
I’m wondering whether it’s worth installing the beta distribution or rather 
uninstalling SIP on each of these many machines.

Also is there any documentation on any specific bugs to watch out for with El 
Capitan and FreeSurfer 5.3?  I’ve been running some functions and haven’t found 
any errors yet.  

Thank you,
Shady El Damaty

PS - how does FreeSurfer 6 plan to get around SIP?
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[Freesurfer] Slice order default

2016-01-28 Thread Rodriguez-Thompson, Anais

Hi Freesurfer experts,

I just starting using slice time correction with a given slice order during 
pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -so 
siemens -fwhm 5 -per-run

Previously I had been using the same command, but without the -so designation. 
Out of curiosity, without that flag was it running slice time correction by 
default? And if it was, what slice order was it using by default?

Thanks,
Anais
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Re: [Freesurfer] FreeSurfer 6 Release Date & El Capitan SIP issues

On 01/28/2016 01:11 PM, Shady El Damaty wrote:
> Hi,
>
> I was curious to know what the tentative release date for FreeSurfer 6 is.  
> I’m currently running FreeSurfer on multiple machines with El Capitan 
> installed and I’m wondering whether it’s worth installing the beta 
> distribution or rather uninstalling SIP on each of these many machines.
>

The release date for FreeSurfer 6 has been hard to nail down but we are 
in the final stages. I hesitate to give a solid date but I would say a 
month is a fair estimate.

> Also is there any documentation on any specific bugs to watch out for with El 
> Capitan and FreeSurfer 5.3?  I’ve been running some functions and haven’t 
> found any errors yet.
>

I would only expect you to encounter errors if you were calling scripts 
which call freesurfer binaries (e.g. recon-all). If your just calling 
the binaries themselves then those should run successfully.

>
> PS - how does FreeSurfer 6 plan to get around SIP?

We plan on getting around it using two methods. 1) creating wrapper 
scripts for some binaries. 2) Adding a source file in existing scripts 
to recreate the library path that were stripped by SIP.

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>
>
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Re: [Freesurfer] Fw: Gray matter intensity

2016-01-28 Thread Sabrina Yu

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57

Figure 1 (c). The mean maps of signal intensity.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Thursday, January 28, 2016 10:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Gray matter intensity

which figure(s) in particular?

On 01/28/2016 01:41 PM, Sabrina Yu wrote:
> Hi,
>
> Sorry for bringing this thread up again. Referring back to the figure in the 
> Salat paper, what map do I load as an overlay to get the intensity maps? How 
> do I generate these maps?
>
> Thank you,
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, December 21, 2015 10:08 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> freeview or tksurfer. Load the relevant map as an overlay
>
> On 12/21/2015 12:57 PM, Sabrina Yu wrote:
>> Hello,
>>
>> Thank you for the very helpful replies! I have another quick question. Which 
>> commands would I use to generate images like the ones  in Figure 1 (C) 
>> generated in the Salat paper 
>> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>>
>> Thank you
>> Sabrina
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Tuesday, December 15, 2015 10:10 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>
>> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>>> Hi,
>>>
>>>
>>> Just following up on my previous email (see below) as I have not yet
>>> heard back. I also have another question regarding the lh.wm.mgh and
>>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>>> overlays on T1 brain scans?
>>>
>> If you want to view them on a volume instead of a surface, you can use
>> mri_surf2vol
>>> Thank you very much.
>>>
>>>
>>>
>>> 
>>> *From:* Sabrina Yu
>>> *Sent:* Thursday, December 10, 2015 2:47 PM
>>> *To:* Freesurfer support list
>>> *Subject:* Gray matter intensity
>>>
>>> Hello,
>>>
>>>
>>>
>>> I have been following the instructions in this email thread:
>>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>>> 
>>>  And
>>> have successfully gotten the wm-gm signal intensity contrast, but
>>> now have a few questions regarding signal intensity for white matter
>>> and gray matter intensity.
>>>
>>>
>>> 1) Does the wmparc.stats contain mean white matter intensity values
>>> for each ROI?
>>>
>> Yes
>>> 2) Is it possible to extract these same mean intensity values for gray
>>> matter? There is no gmparc.stats file. We know that it's possible to
>>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>>> great if there was a more direct way to get this data.
>>>
>> There is not one by default that includes the cortical parcellation. You
>> can create your own with mri_segstats passing it the aparc+aseg.mgz as
>> the segmentation. Look in the recon-all.log file for the command line
>> that creates the aseg.stats or wmparc.stats. You will probably need to
>> change the --ctab flag to --ctab-default (no argument)
>>> Thank you,
>>>
>>> Sabrina Yu
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>>

Re: [Freesurfer] Fw: Gray matter intensity

which figure(s) in particular?

On 01/28/2016 01:41 PM, Sabrina Yu wrote:
> Hi,
>
> Sorry for bringing this thread up again. Referring back to the figure in the 
> Salat paper, what map do I load as an overlay to get the intensity maps? How 
> do I generate these maps?
>
> Thank you,
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, December 21, 2015 10:08 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> freeview or tksurfer. Load the relevant map as an overlay
>
> On 12/21/2015 12:57 PM, Sabrina Yu wrote:
>> Hello,
>>
>> Thank you for the very helpful replies! I have another quick question. Which 
>> commands would I use to generate images like the ones  in Figure 1 (C) 
>> generated in the Salat paper 
>> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>>
>> Thank you
>> Sabrina
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Tuesday, December 15, 2015 10:10 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>
>> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>>> Hi,
>>>
>>>
>>> Just following up on my previous email (see below) as I have not yet
>>> heard back. I also have another question regarding the lh.wm.mgh and
>>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>>> overlays on T1 brain scans?
>>>
>> If you want to view them on a volume instead of a surface, you can use
>> mri_surf2vol
>>> Thank you very much.
>>>
>>>
>>>
>>> 
>>> *From:* Sabrina Yu
>>> *Sent:* Thursday, December 10, 2015 2:47 PM
>>> *To:* Freesurfer support list
>>> *Subject:* Gray matter intensity
>>>
>>> Hello,
>>>
>>>
>>>
>>> I have been following the instructions in this email thread:
>>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>>> 
>>>  And
>>> have successfully gotten the wm-gm signal intensity contrast, but
>>> now have a few questions regarding signal intensity for white matter
>>> and gray matter intensity.
>>>
>>>
>>> 1) Does the wmparc.stats contain mean white matter intensity values
>>> for each ROI?
>>>
>> Yes
>>> 2) Is it possible to extract these same mean intensity values for gray
>>> matter? There is no gmparc.stats file. We know that it's possible to
>>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>>> great if there was a more direct way to get this data.
>>>
>> There is not one by default that includes the cortical parcellation. You
>> can create your own with mri_segstats passing it the aparc+aseg.mgz as
>> the segmentation. Look in the recon-all.log file for the command line
>> that creates the aseg.stats or wmparc.stats. You will probably need to
>> change the --ctab flag to --ctab-default (no argument)
>>> Thank you,
>>>
>>> Sabrina Yu
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> 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:

Re: [Freesurfer] recon-all: core dumped error

Yes the newest development version will solve it. You can download the 
latest development version using the following link:

   ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/

Or you can download any of the individual binaries using the following link:

   ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/

Hope this helps,

-Zke

On 01/28/2016 01:40 PM, Fengji Geng wrote:
> Hi Bruce,
>
> Below is our hardware/software information. Also curious, will install
> the newest development  version of fs 6.0 solve our problem either?
>
> Thanks a lot!
>
> Linux 2.6.32-573.12.1.el6.x86_64
>
> LSB Version:
> :base-4.0-amd64:base-4.0-ia32:base-4.0-noarch:core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch
>
> Distributor ID:RedHatEnterpriseServer
>
> Description:Red Hat Enterprise Linux Server release 6.7 (Santiago)
>
> Release:   6.7
>
> Codename:Santiago
>
> freesurfer-Linux-centos6_x86_64-dev-20151215
>
> 
>
> Hi Fengji,
>
> it's called mris_ca_label, and yes, that is what I mean. If you tell us
> your hardware/software environment Zeke can get you a binary
>
> On Thu, 28 Jan 2016,
>
> Fengji Geng wrote:
>
>  >
>
>  > Hi Bruce,
>
>  >
>
>  > Did you mean an updated version of mri_parcellate? If so, it would be
> great.
>
>  >
>
>  > Thanks!
>
>  >
>
>  > ?
>
>  >
>
>  > 
>
>  >
>
>  > ?
>
>  >
>
>  > ?
>
>  >
>
>  > Hi Fengji
>
>  >
>
>  > ?
>
>  >
>
>  > this is a known bug in mris_parcellate. We can give you an updated
>
>  > version
>
>  >
>
>  > if you want, but you should probably rerun all your subjects using it.
>
>  > The
>
>  >
>
>  > good news is that it's fast - just a couple of min/hemi
>
>  >
>
>  > ?
>
>  >
>
>  > cheers
>
>  >
>
>  > Bruce
>
>  >
>
>  > ? On Tue, 26 Jan
>
>  >
>
>  > 2016, Fengji Geng wrote:
>
>  >
>
>  > ?
>
>  >
>
>  > > Hello fs experts,
>
>  >
>
>  > >
>
>  >
>
>  > > We ran a command like ?recon-all -all -s HMN002
>
>  > -hippocampal-subfields-T1T2
>
>  >
>
>  > > HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core
> dumped)?
>
>  >
>
>  > > (which is also attached below). The error log file is also attached
> here.?
>
>  >
>
>  > >
>
>  >
>
>  > > Error msg:
>
>  >
>
>  > >-
>
>  > >--
>
>  >
>
>  > > --
>
>  >
>
>  > > setting seed for random number generator to 1234
>
>  >
>
>  > > using ../mri/aseg.presurf.mgz aseg volume to correct midline
>
>  >
>
>  > > $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
>
>  >
>
>  > > ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $
>
>  >
>
>  > > reading
>
>  > > atlasfrom/cell_root/software/freesurfer/dev/sys/average/lh.curvature
>
>  > > .buckner40.f
>
>  > ille
>
>  >
>
>  > > d.desikan_killiany.2010-03-25.gcs...
>
>  >
>
>  > > reading color table from GCSA file
>
>  >
>
>  > > average std = 1.0?? using min determinant for regularization = 0.011
>
>  >
>
>  > > 0 singular and 384 ill-conditioned covariance matrices regularized
>
>  >
>
>  > > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
>
>  >
>
>  > > labeling surface...
>
>  >
>
>  > > 1592 labels changed using aseg
>
>  >
>
>  > > relabeling using gibbs priors...
>
>  >
>
>  > > 000:?? 2975 changed, 134786 examined...
>
>  >
>
>  > > 001:??? 698 changed, 12707 examined...
>
>  >
>
>  > > 002:??? 152 changed, 3873 examined...
>
>  >
>
>  > > 003: 50 changed, 880 examined...
>
>  >
>
>  > > 004: 29 changed, 284 examined...
>
>  >
>
>  > > 005: 16 changed, 164 examined...
>
>  >
>
>  > > 006:? 7 changed, 87 examined...
>
>  >
>
>  > > 007:? 1 changed, 42 examined...
>
>  >
>
>  > > 008:? 0 changed, 4 examined...
>
>  >
>
>  > > 206 labels changed using aseg
>
>  >
>
>  > > 000: 105 total segments, 64 labels (264 vertices) changed
>
>  >
>
>  > > 001: 43 total segments, 4 labels (14 vertices) changed
>
>  >
>
>  > > 002: 39 total segments, 0 labels (0 vertices) changed
>
>  >
>
>  > > 1 filter iterations complete (10 requested, 0 changed)
>
>  >
>
>  > > Abort (core dumped)
>
>  >
>
>  > > Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov
>
>  > > 23
>
>  >
>
>  > > 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux
>
>  >
>
>  > >
>
>  >
>
>  > > recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST
>
>  > > 2016
>
>  >
>
>  > >
>
>  >
>
>  > > Our freesurfer information:
>
>  >
>
>  > >  freesurfer-Linux-centos6_x86_64-dev-20151215 
>
>  >
>
>  > > Setting up environment for FreeSurfer/FS-FAST (and FSL)
>
>  >
>
>  > > FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys
>
>

Re: [Freesurfer] Slice order default

2016-01-28 Thread Rodriguez-Thompson, Anais

OK, that's good to know. Thanks!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, January 28, 2016 1:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Slice order default

slice time correction is not used by default

On 01/28/2016 01:16 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts,
>
> I just starting using slice time correction with a given slice order during 
> pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -so 
> siemens -fwhm 5 -per-run
>
> Previously I had been using the same command, but without the -so 
> designation. Out of curiosity, without that flag was it running slice time 
> correction by default? And if it was, what slice order was it using by 
> default?
>
> Thanks,
> Anais
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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Re: [Freesurfer] HSF in 5.3

2016-01-28 Thread Eugenio Iglesias

Hi Alan, 
can you please list the files in the mri directory of any of the subjects and 
send me the output? 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Alan Francis"  
To: "Eugenio Iglesias"  
Cc: "Freesurfer support list"  
Sent: Thursday, January 28, 2016 9:18:46 PM 
Subject: Re: HSF in 5.3 

Hi Eugenio: 

As you advised, I ran the following command: 

afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024 
Nicotine_HSF.txt 
Gathering results from subjects in: 
/Users/afrancis/Desktop/Connectome/HSF/ 
Using the suffix name: 
Smoke_e024 
And writing them to: 
Nicotine_HSF.txt 

However, when I opened the Nicotine_HSF.txt, there was nothing there. The 
Subjects directory is the same folder. 

Please advice - thanks so much, 

Alan 

On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias < e.igles...@bcbl.eu > 
wrote: 



Hi Alan, 
the subfield module is not present in 5.3; you'll need to download the 
development version (or wait until 6.0 is released, which should be pretty 
soon=. 
Cheers, 
Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Alan Francis" < alandarkene...@gmail.com > 
To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu >, "eiglesias" < 
eigles...@bcbl.eu > 
Sent: Friday, December 11, 2015 6:36:42 PM 
Subject: HSF in 5.3 

Hi Eugenio: 
I am trying to run the HSF method on 42 subjects. The FS version on our cluster 
is 5.3. However when I use the following command I get an error message. 



[alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields 

ERROR: Flag -hippocampal-subfields unrecognized. 

-s Smoke_d004 -hippocampal-subfields 

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 
x86_64 x86_64 GNU/Linux 




recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015 




For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 





I tried adding the -hippocampal-subfields-T1 but that did not work too. 




thanks, 




Alan 
-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 

Alan N . Francis PhD 
NIDA T32 Fellow in Computational Neuroscience 
Brain Imaging Center 
McLean Hospital 
Harvard Medical School 
115 Mill Street, Belmont, MA 02478 
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 







-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 

Alan N . Francis PhD 
NIDA T32 Fellow in Computational Neuroscience 
Brain Imaging Center 
McLean Hospital 
Harvard Medical School 
115 Mill Street, Belmont, MA 02478 
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| 

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Re: [Freesurfer] Wm correction

Hi Bruce,Thanks for your reply, I will take look on aseg volume.
Best,Mrayam

On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
 wrote:

 Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> Ventricle. As you can see in the image attached, the big part is excluded in
> both hemisphere. I tried to fill it by editing wm volume but the problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] HSF in 5.3

2016-01-28 Thread Alan Francis

Hi Eugenio:

As you advised, I ran the following command:

afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024
Nicotine_HSF.txt
Gathering results from subjects in:
   /Users/afrancis/Desktop/Connectome/HSF/
Using the suffix name:
   Smoke_e024
And writing them to:
   Nicotine_HSF.txt

However, when I opened the Nicotine_HSF.txt, there was nothing there. The
Subjects directory is the same folder.

Please advice - thanks so much,

Alan

On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias 
wrote:

> Hi Alan,
> the subfield module is not present in 5.3; you'll need to download the
> development version (or wait until 6.0 is released, which should be pretty
> soon=.
> Cheers,
> Eugenio
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Alan Francis" 
> *To: *"Freesurfer support list" ,
> "eiglesias" 
> *Sent: *Friday, December 11, 2015 6:36:42 PM
> *Subject: *HSF in 5.3
>
> Hi Eugenio:
> I am trying to run the HSF method on 42 subjects. The FS version on our
> cluster is 5.3. However when I use the following command I get an error
> message.
>
> [alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields
>
> ERROR: Flag -hippocampal-subfields unrecognized.
>
> -s Smoke_d004 -hippocampal-subfields
>
> Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013
> x86_64 x86_64 x86_64 GNU/Linux
>
>
> recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015
>
>
> For more details, see the log file
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> I tried adding the  -hippocampal-subfields-T1 but that did not work too.
>
>
> thanks,
>
>
> Alan
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> *Alan N. Francis PhD*
> NIDA T32  Fellow in Computational Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu 
> afran...@mclean.harvard.edu
>
>
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Fwd: hardware question

2016-01-28 Thread R Edgar

On 28 January 2016 at 11:51, Z K  wrote:
> How many cores/processors? In an earlier email you stated that you
> wanted to process many recons at the same time. If this is the case than
> the number of processors would be the limiting factor.
>
> FYI: Freesurfer version 6 will include a "-parallel" flag which will use
> 4 processors (by to default) to proces both the left and right
> hemispheres of the brain. This drastically reduces runtime and the
> expense of resources.

I'd add that that GPU should be very capable of running the
CUDA-accelerated applications as well. I'd be interested in seeing the
mri_ca_register times.

Regards,

Richard
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Re: [Freesurfer] Reading values from overlays with PETcoreg



On 01/28/2016 06:50 PM, Pradeep wrote:
> Hello Doug,
>
> I have used the gtmseg with --keep-cc  flag and the corresponding ctab 
> files showed the labels but the mri_gtmpvc step failed.
> 
> Loading seg for gtm gtmseg.mgz
> Loading seg ctab gtmseg.ctab
> Reading gtmseg.lta
> Replacing 18
> ERROR: CheckSegTissueType() no entry for seg 192
> Failed tissue type check
> 
What is your mri_gtmpvc command line? What is the rest of the terminal 
output?
> My objective is to use the combination of all CC's as a reference 
> region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, 
eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251
this will cause all segments of the CC to appear to be a single segment 
(251).
>
> Also, I read in the previous email discussions that the default 
> ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with 
> another ROI as a reference region,
> would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
>
> Thanks,
> Pradeep
>
> On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve 
> > wrote:
>
>
> If you want to use partial volume correction, then you are better off
> using mri_gtmpvc with the bbr registration, something like
>
> 1. To start, run
>
> gtmseg --s subject
>
> This will take a couple of hours and produces some files needed
> for GTM
> PVC (which is used for GTM, MG, RBV).
>
> 2. You'd then register the PET to the anatomical with bbregister
> (probably with --t2 weighting). Make sure to save the output as an LTA
> (--lta). I usually use the mean TAC as the input. You can do this in
> parallel with #1.
>
> 3. You'd then run mri_gtmpvc, something like
>
> mri_gtmpvc --i pet.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg
> gtmseg.mgz
> --reg reg.lta --default-seg-merge  --o gtmpvc.output
>
> PSF is the point-spread FWHM of the scanner; reg.lta is the
> registration from #2. By default, this will scale by pons. The output
> will be gtm.stats.dat and gtm.nii.gz. They both basically have the
> same information. gtm.stats.dat is an easy to read text file. Where
> each row is an ROI, something like:
>
> 9   17 Left-Hippocampussubcort_gm   473
> 174.0831.406   0.1216
>
> 9 = nineth row
> 17 = index for RO
> Left-Hippocampus = name of ROI
> subcort_gm = tissue class
> 473 = number of PET voxels in the ROI
> 174 = variance reduction factor for ROI (based on GLM/SGTM)
> 1.406 = PVC uptake of ROI relative to Pons
> 0.1216 = resdiual varaince across voxels in the ROI
>
> gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value
> is the PVC uptake of ROI relative to Pons. These can easily be
> concatenated together (mri_concat) and used as input to mri_glmfit
> for group analysis.
>
>
>
>
> On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
> > Dear Freesurfer experts!
> >
> > I am currently working on PET analysis using FS
> >
> > I coregistered my PET with the processed MR using bbregister,
> > transfered it to a surface using mri_vol2surf
> > and now createt an overlay in freeview with the lh.inflated and
> used the
> > labels from the lh.aparc.a2009s.annot file.
> >
> > In freeview i get the corresponding BP value for each vertex now but
> > is there a way to get a list of vertices with the corresponding
> BP value
> > and the corresponding ROI this vertex belongs to?
> > Or is there a better to do this analyis?
> >
> > Many thanks in advance!
> >
> > Benjamin
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the

Re: [Freesurfer] Reading values from overlays with PETcoreg

2016-01-28 Thread Pradeep

Hello Doug,

I have used the gtmseg with --keep-cc  flag and the corresponding ctab
files showed the labels but the mri_gtmpvc step failed.

Loading seg for gtm gtmseg.mgz
Loading seg ctab gtmseg.ctab
Reading gtmseg.lta
Replacing 18
ERROR: CheckSegTissueType() no entry for seg 192
Failed tissue type check

My objective is to use the combination of all CC's as a reference region
and obtain the PVC results, which would be listed in gtm.stats.dat

Also, I read in the previous email discussions that the default ref-region
Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a
reference region,
would it be OK take a ratio of the ROI's in gtm.stats.dat table.

Thanks,
Pradeep

On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve 
wrote:

>
> If you want to use partial volume correction, then you are better off
> using mri_gtmpvc with the bbr registration, something like
>
> 1. To start, run
>
> gtmseg --s subject
>
> This will take a couple of hours and produces some files needed for GTM
> PVC (which is used for GTM, MG, RBV).
>
> 2. You'd then register the PET to the anatomical with bbregister
> (probably with --t2 weighting). Make sure to save the output as an LTA
> (--lta). I usually use the mean TAC as the input. You can do this in
> parallel with #1.
>
> 3. You'd then run mri_gtmpvc, something like
>
> mri_gtmpvc --i pet.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg gtmseg.mgz
> --reg reg.lta --default-seg-merge  --o gtmpvc.output
>
> PSF is the point-spread FWHM of the scanner; reg.lta is the
> registration from #2. By default, this will scale by pons.  The output
> will be gtm.stats.dat and gtm.nii.gz. They both basically have the
> same information. gtm.stats.dat is an easy to read text file. Where
> each row is an ROI, something like:
>
> 9   17 Left-Hippocampussubcort_gm   473
> 174.0831.406   0.1216
>
> 9 = nineth row
> 17 = index for RO
> Left-Hippocampus = name of ROI
> subcort_gm = tissue class
> 473 = number of PET voxels in the ROI
> 174 = variance reduction factor for ROI (based on GLM/SGTM)
> 1.406 = PVC uptake of ROI relative to Pons
> 0.1216 = resdiual varaince across voxels in the ROI
>
> gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value
> is the PVC uptake of ROI relative to Pons. These can easily be
> concatenated together (mri_concat) and used as input to mri_glmfit
> for group analysis.
>
>
>
>
> On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
> > Dear Freesurfer experts!
> >
> > I am currently working on PET analysis using FS
> >
> > I coregistered my PET with the processed MR using bbregister,
> > transfered it to a surface using mri_vol2surf
> > and now createt an overlay in freeview with the lh.inflated and used the
> > labels from the lh.aparc.a2009s.annot file.
> >
> > In freeview i get the corresponding BP value for each vertex now but
> > is there a way to get a list of vertices with the corresponding BP value
> > and the corresponding ROI this vertex belongs to?
> > Or is there a better to do this analyis?
> >
> > Many thanks in advance!
> >
> > Benjamin
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Crashing with Fedora 23

After a bit of investigating, Ive determined that the error you've 
encountered is due to a conflict with the mni tools shipped with 
freesurfer v5.3, and the latest version of perl (version 5.22, shipped 
with Fedora 23).

This has been fixed in the dev version of freesurfer and thus will be 
fixed in the upcoming release of freesurfer version 6.0. So you 
basically have 2 options if you want to use freesurfer on your platform:

1) Update to the newest Development Version of freesurfer:

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

Or, 2) Use perlbrew (http://perlbrew.pl/) to role back your version of perl:

   $> \curl -L http://install.perlbrew.pl | bash
   $> perlbrew install perl-5.20.1
   $> perlbrew switch perl-5.20.1

Hope this helps.

-Zeke








On 01/26/2016 11:09 AM, Barron, Daniel wrote:
> Hi ZK,
> It was SLED 11.4. Thanks for looking into it. Appreciate your time.
> db
>
> On 1/26/16, 11:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Z K"  zkauf...@nmr.mgh.harvard.edu> wrote:
>
>> This appears to be something specific with Fedora 23... I will attempt
>> to duplicate on a Fedora 23 virtual machine as I dont have one handy.
>> Can you recall what version you were running before you upgraded to
>> Fedora 23 when recon-all when running successfully?
>>
>> On 01/25/2016 02:05 PM, Barron, Daniel wrote:
>>> Hi Martin,
>>> We¹ve got the tcsh installed and seems to be working.  Can¹t find a
>>> similar report on the list serve, so I¹ve attached the bug report info
>>> below plus the orig_nu.log output, which is where the script is
>>> crashing. Please help!
>>> Cheers,
>>> Daniel
>>>
>>> *Output from buggr:*
>>> FREESURFER_HOME: /home/freesurfer
>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>> RedHat release: Fedora release 23 (Twenty Three)
>>> Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64
>>> Subject Name: 2_03T_N12_12_18441
>>>
>>> *Command I¹m entering:*
>>> for subject in 2_03T_N12_12_18441; do
>>> recon-all -subjid ${subject} -all -hippo-subfields
>>> done
>>>
>>> *Error Message (from recon-all.error):*
>>> --
>>> SUBJECT 2_03T_N12_12_18441
>>> DATE Mon Jan 25 18:40:30 GMT 2016
>>> USER dsbarron
>>> HOST psyws26.psych.ox.ac.uk
>>>
>>> >> uk=AwMFaQ=-dg2m7zWuuDZ0MUcV7Sdqw=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>> h34fYFosM=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI=gsKhS9Mym34PR3U
>>> Xiv5lzMEopfAGkdYdn_1AEwRrd74=>
>>> PROCESSOR x86_64
>>> OS Linux
>>> Linux psyws26.psych.ox.ac.uk
>>>
>>> >> uk=AwMFaQ=-dg2m7zWuuDZ0MUcV7Sdqw=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>> h34fYFosM=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI=gsKhS9Mym34PR3U
>>> Xiv5lzMEopfAGkdYdn_1AEwRrd74=> 4.3.3-300.fc23.x86_64
>>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>>> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
>>> /home/freesurfer/bin/recon-all
>>> PWD /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri
>>> CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>>> --no-rescale --i orig.mgz --o orig_nu.mgz
>>>
>>> #
>>> *recon-all.log:*
>>>
>>> Mon Jan 25 18:43:18 GMT 2016
>>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441
>>> /home/freesurfer/bin/recon-all
>>> -subjid 2_03T_N12_12_18441 -all -hippo-subfields
>>> subjid 2_03T_N12_12_18441
>>> setenv SUBJECTS_DIR /home/dsbarron/Schmidt/Freesurfer
>>> FREESURFER_HOME /home/freesurfer
>>> Actual FREESURFER_HOME /home/freesurfer
>>> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>> Linux psyws26.psych.ox.ac.uk
>>>
>>> >> uk=AwMFaQ=-dg2m7zWuuDZ0MUcV7Sdqw=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>> h34fYFosM=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI=gsKhS9Mym34PR3U
>>> Xiv5lzMEopfAGkdYdn_1AEwRrd74=> 4.3.3-300.fc23.x86_64
>>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>>> cputime  unlimited
>>> filesize unlimited
>>> datasize unlimited
>>> stacksize8192 kbytes
>>> coredumpsize 0 kbytes
>>> memoryuseunlimited
>>> vmemoryuse   unlimited
>>> descriptors  1024
>>> memorylocked 64 kbytes
>>> maxproc  128183
>>> maxlocks unlimited
>>> maxsignal128183
>>> maxmessage   819200
>>> maxnice  0
>>> maxrtprio0
>>> maxrttimeunlimited
>>>
>>> totalusedfree  shared  buff/cache
>>> available
>>> Mem:   32901484 2311624 1288116  12189629301744
>>> 29874168
>>> Swap:  16515068 134492415170144
>>>
>>> 
>>> program versions used
>>> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
>>> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
>>> mri_convert -all-info
>>>

Re: [Freesurfer] Wm correction

Hi Bruce,
How can I download version 6?

Best,Maryam

Regards,Maryam Kouchakidivkolaei 

On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
 wrote:

 Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> Ventricle. As you can see in the image attached, the big part is excluded in
> both hemisphere. I tried to fill it by editing wm volume but the problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] fast_selxavg3 error when Octave is used

2016-01-28 Thread m.abouelyazid

Yes, it exists in the location you mentioned…

From: Douglas N Greve
Sent: Friday, January 29, 2016 2:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3 error when Octave is used

Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ?

On 01/28/2016 07:16 AM, m.abouelya...@gmail.com wrote:
>
> Since I am a windows user I got the Virtualbox version of FreeSurfer 
> and to use fs fast, I installed Octave on the virtual machine, I set 
> the environment variables and then when I run the command
>
> selxavg3-sess -analysis rtopy.lh -sf sessid
>
> which runs a retinotopy analysis, I get the following error:
>
> sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx
>
> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis 
> rtopy.lh -sf sessid
>
> error: `fast_fileexists' undefined near line 5 column 4
>
> --
>
> ERROR: fast_selxavg3() failed\n
>
> Any idea of the cause of this error and how to run around?
>
> Thank you,
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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[Freesurfer] wm correction

Hi Bruce,
I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral 
Ventricle. As you can see in the image attached, the big part is excluded in 
both hemisphere. I tried to fill it by editing wm volume but the problem still 
exists.Do you have any suggestion?Thanks,Maryam
 






 
 test_vumc_158_rh.png
 test_vumc_158_lh.png


 

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[Freesurfer] Fwd: hardware question

2016-01-28 Thread Joost Janssen

Hi,

We're thinking of buying a computer with the main goal simultaneous
processing of 'recon-all's'. the computer cannot be a 'cluster' and must be
linux. These specs looked good to us:

- Intel Core i7-5820K 3.3Ghz

- Asus X99-A

- Arctic Cooling Freezer A30 CPU Cooler

- G.Skill Aegis DDR4 2400 PC4-19200 16GB CL15

- Samsung 850 Evo SSD Series 500GB SATA3

- Toshiba 4TB 7200rpm SATA3

- Aerocool Aero 800 Negra USB 3.0

- AeroCool KCAS 700W 80 Plus Bronze

- Asus GeForce Strix GTX 960 DirectCU II OC 4GB GDDR5

Are there things we can improve at? Thanks for any advice!
-joost
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[Freesurfer] fast_selxavg3 error when Octave is used

2016-01-28 Thread m.abouelyazid

Since I am a windows user I got the Virtualbox version of FreeSurfer and to use 
fs fast, I installed Octave on the virtual machine, I set the environment 
variables and then when I run the command

selxavg3-sess -analysis rtopy.lh -sf sessid

which runs a retinotopy analysis, I get the following error:

sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx
sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis rtopy.lh -sf 
sessid
error: `fast_fileexists' undefined near line 5 column 4
--
ERROR: fast_selxavg3() failed\n

Any idea of the cause of this error and how to run around?

Thank you,
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Re: [Freesurfer] Longitudinal analysis--mass univariate

2016-01-28 Thread John Anderson

Thanks a lot D martin for your quick answer.

Regarding my patients I have two groups but the subject in every group have differnt time points. i.e Group-patients 1: I have 100 patients some scanned three times and some four times the rest at least two times.

Group-Patients 2: is consisted of 75 patients some also some scanned three times and some four times the rest at least two times.

Is LME -- mas usnivariate still workable with out a bias ?

Bests,
John

Sent: Thursday, January 28, 2016 at 6:51 AM
From: "Martin Reuter"
To: "Freesurfer support list"
Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate

Hi John,

you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3.

You can compare the atrophy across these two groups easily with LME. Or you can also test if the rate is different from zero in each individual group.

You will never be able to compute atrophy rates for your control group (as you only have a single time point for them) so you cannot compare with them either.

Best, Martin

On Jan 28, 2016, at 12:23 PM, John Anderson wrote:

Hi Dr Martin,

I have two groups of patients and one group of controls.

The patients scanned multiple times but the number of time points is different between the subjects.

The controls have only one time point.

I aim to :

1. I wanted to study the changes in cortical thickness over time in each group of patients.

2. I wanted to compare the change in cortical thickness between patients and controls over time.

I followed wiki and I choose LME to run the analysis.

My questions are:

1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.

2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach.

Bests,
John

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[Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05 {Disarmed}

2016-01-28 Thread Erik Lindberg

Dear Bruce and Freesufers,


I get the following message:


surfer: Interpreting overlay volume
/media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glmdir/Gend/thresholded.mgh
as encoded scalar volume.


the two volumes I tried to convert:

1)

Volume information for sig.mgh
  type: MGH
dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   0., z_a =   1., c_a =
0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
0.

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 81921.
0.   0.   1.-0.5000
0.  -1.   0. 0.5000
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0. 81921.
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 0.5000
0.   0.   0. 1.


2)


Volume information for cache.th13.abs.sig.cluster.mgh
  type: MGH
dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   0., z_a =   1., c_a =
0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
0.

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 81921.
0.   0.   1.-0.5000
0.  -1.   0. 0.5000
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0. 81921.
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 0.5000
0.   0.   0. 1.


Although both these overlays have significant areas - nothing appears on
the binarized version after the conversion


Best wishes,

Olof Lindberg

Olof Lindberg PhD
Novum plan 5
NVS department section clinical geriatrics
14186 Stockholm
+46722255711
http://www.oloflindberg.se

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Re: [Freesurfer] Longitudinal analysis--mass univariate

2016-01-28 Thread Martin Reuter

Hi John,

you should check if the number of time points per subject is relatively random 
across your two patient groups. You don’t want a bias, let’s say one patient 
group with 2 tp and the other with 3.

You can compare the atrophy across these two groups easily with LME. Or you can 
also test if the rate is different from zero in each individual group. 

You will never be able to compute atrophy rates for your control group (as you 
only have a single time point for them) so you cannot compare with them either.

Best, Martin

> On Jan 28, 2016, at 12:23 PM, John Anderson  wrote:
> 
> Hi Dr Martin,
> I have two groups of patients and one group of controls.
> The patients scanned multiple times but the number of time points is 
> different between the subjects.
> The controls have only one time point.
>  
> I aim to :
> 1. I wanted to study the changes in cortical thickness over time in each 
> group of patients.
> 2. I wanted to compare the change in cortical thickness between patients and 
> controls over time.
>  
> I followed wiki and I choose LME to run the analysis.
> My questions are:
> 1. Can I use mass univariate analysis to check the changes in cortical 
> thickness over time in only one group of patients. The example In wiki was 
> for four groups.
> 2. Can I do a comparison in cortical thickness over time between controls ( 
> who have  only one time point ) and patients using mass univariate approach.
>  
> Bests,
> John 
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[Freesurfer] Longitudinal analysis--mass univariate

2016-01-28 Thread John Anderson

Hi Dr Martin,

I have two groups of patients and one group of controls.

The patients scanned multiple times but the number of time points is different between the subjects.

The controls have only one time point.

 

I aim to :

1. I wanted to study the changes in cortical thickness over time in each group of patients.

2. I wanted to compare the change in cortical thickness between patients and controls over time.

 

I followed wiki and I choose LME to run the analysis.

My questions are:

1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.

2. Can I do a comparison in cortical thickness over time between controls ( who have  only one time point ) and patients using mass univariate approach.
 

Bests,
John 
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Re: [Freesurfer] mris_preproc on zipped data

no, sorry

On 01/28/2016 11:11 AM, Lars M. Rimol wrote:
> Hi,
>
> I have a large amount of data (FS scanworkups) where all the files within
> every subject's directory are zipped. Is there a way to run mris_preproc on
> zipped data?
> For instance, mris_preproc crashes because it can't find lh.thickness
> unless I unzip it
>
>
> Thank you!
>
>
>
>
>
>
> sincerely yours,
>
> Lars M. Rimol, PhD
> Senior researcher,
> Norwegian Advisory Unit for functional MRI
> Department of Radiology,
> St. Olav's University hospital,
> 7006 Trondheim,
> Norway
>
>
>
>
>
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Re: [Freesurfer] Slice order default

slice time correction is not used by default

On 01/28/2016 01:16 PM, Rodriguez-Thompson, Anais wrote:
> Hi Freesurfer experts,
>
> I just starting using slice time correction with a given slice order during 
> pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -so 
> siemens -fwhm 5 -per-run
>
> Previously I had been using the same command, but without the -so 
> designation. Out of curiosity, without that flag was it running slice time 
> correction by default? And if it was, what slice order was it using by 
> default?
>
> Thanks,
> Anais
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>
>

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Fax: 617-726-7422

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Re: [Freesurfer] recon-all: core dumped error

2016-01-28 Thread Fengji Geng

Hi Bruce,
Below is our hardware/software information. Also curious, will install the 
newest development  version of fs 6.0 solve our problem either?

Thanks a lot!


Linux 2.6.32-573.12.1.el6.x86_64
LSB Version:   
:base-4.0-amd64:base-4.0-ia32:base-4.0-noarch:core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch
Distributor ID:RedHatEnterpriseServer
Description:Red Hat Enterprise Linux Server release 6.7 (Santiago)
Release:   6.7
Codename:Santiago


freesurfer-Linux-centos6_x86_64-dev-20151215




Hi Fengji,

it's called mris_ca_label, and yes, that is what I mean. If you tell us your 
hardware/software environment Zeke can get you a binary



On Thu, 28 Jan 2016,

Fengji Geng wrote:



>

> Hi Bruce,

>

> Did you mean an updated version of mri_parcellate? If so, it would be great.

>

> Thanks!

>

> ?

>

> 

>

> ?

>

> ?

>

> Hi Fengji

>

> ?

>

> this is a known bug in mris_parcellate. We can give you an updated

> version

>

> if you want, but you should probably rerun all your subjects using it.

> The

>

> good news is that it's fast - just a couple of min/hemi

>

> ?

>

> cheers

>

> Bruce

>

> ? On Tue, 26 Jan

>

> 2016, Fengji Geng wrote:

>

> ?

>

> > Hello fs experts,

>

> >

>

> > We ran a command like ?recon-all -all -s HMN002

> -hippocampal-subfields-T1T2

>

> > HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)?

>

> > (which is also attached below). The error log file is also attached here.?

>

> >

>

> > Error msg:

>

> >-

> >--

>

> > --

>

> > setting seed for random number generator to 1234

>

> > using ../mri/aseg.presurf.mgz aseg volume to correct midline

>

> > $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $

>

> > ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $

>

> > reading

> > atlasfrom/cell_root/software/freesurfer/dev/sys/average/lh.curvature

> > .buckner40.f

> ille

>

> > d.desikan_killiany.2010-03-25.gcs...

>

> > reading color table from GCSA file

>

> > average std = 1.0?? using min determinant for regularization = 0.011

>

> > 0 singular and 384 ill-conditioned covariance matrices regularized

>

> > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature

>

> > labeling surface...

>

> > 1592 labels changed using aseg

>

> > relabeling using gibbs priors...

>

> > 000:?? 2975 changed, 134786 examined...

>

> > 001:??? 698 changed, 12707 examined...

>

> > 002:??? 152 changed, 3873 examined...

>

> > 003: 50 changed, 880 examined...

>

> > 004: 29 changed, 284 examined...

>

> > 005: 16 changed, 164 examined...

>

> > 006:? 7 changed, 87 examined...

>

> > 007:? 1 changed, 42 examined...

>

> > 008:? 0 changed, 4 examined...

>

> > 206 labels changed using aseg

>

> > 000: 105 total segments, 64 labels (264 vertices) changed

>

> > 001: 43 total segments, 4 labels (14 vertices) changed

>

> > 002: 39 total segments, 0 labels (0 vertices) changed

>

> > 1 filter iterations complete (10 requested, 0 changed)

>

> > Abort (core dumped)

>

> > Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov

> > 23

>

> > 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux

>

> >

>

> > recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST

> > 2016

>

> >

>

> > Our freesurfer information:

>

> >  freesurfer-Linux-centos6_x86_64-dev-20151215 

>

> > Setting up environment for FreeSurfer/FS-FAST (and FSL)

>

> > FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys

>

> > FSFAST_HOME?? /cell_root/software/freesurfer/dev/sys/fsfast

>

> > FSF_OUTPUT_FORMAT nii.gz

>

> > SUBJECTS_DIR? /export/data/hippocampus/HMN/data

>

> > MNI_DIR?? /cell_root/software/freesurfer/dev/sys/mni

>

> > FSL_DIR?? /cell_root/software/fsl/new/sys

>

> >

>

> > Looking forward to hearing how we can resolve this error. Also,

> > thanks in

>

> > advance.

>

> >

>

> > Best,

>

> >

>

> > - Fengji

>

> >

>

> >

>

> >?

>

> ?

>

> ?

>

> ---

>

> Fengji

>

> ?

>

>

>


---
Fengji

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Re: [Freesurfer] Fw: Gray matter intensity

2016-01-28 Thread Sabrina Yu

Hi, 

Sorry for bringing this thread up again. Referring back to the figure in the 
Salat paper, what map do I load as an overlay to get the intensity maps? How do 
I generate these maps?

Thank you, 
Sabrina


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Monday, December 21, 2015 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:
> Hello,
>
> Thank you for the very helpful replies! I have another quick question. Which 
> commands would I use to generate images like the ones  in Figure 1 (C) 
> generated in the Salat paper 
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>
> Thank you
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, December 15, 2015 10:10 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>> Hi,
>>
>>
>> Just following up on my previous email (see below) as I have not yet
>> heard back. I also have another question regarding the lh.wm.mgh and
>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>> overlays on T1 brain scans?
>>
> If you want to view them on a volume instead of a surface, you can use
> mri_surf2vol
>>
>> Thank you very much.
>>
>>
>>
>> 
>> *From:* Sabrina Yu
>> *Sent:* Thursday, December 10, 2015 2:47 PM
>> *To:* Freesurfer support list
>> *Subject:* Gray matter intensity
>>
>> Hello,
>>
>>
>>
>> I have been following the instructions in this email thread:
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>> 
>>  And
>> have successfully gotten the wm-gm signal intensity contrast, but
>> now have a few questions regarding signal intensity for white matter
>> and gray matter intensity.
>>
>>
>> 1) Does the wmparc.stats contain mean white matter intensity values
>> for each ROI?
>>
> Yes
>> 2) Is it possible to extract these same mean intensity values for gray
>> matter? There is no gmparc.stats file. We know that it's possible to
>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>> great if there was a more direct way to get this data.
>>
> There is not one by default that includes the cortical parcellation. You
> can create your own with mri_segstats passing it the aparc+aseg.mgz as
> the segmentation. Look in the recon-all.log file for the command line
> that creates the aseg.stats or wmparc.stats. You will probably need to
> change the --ctab flag to --ctab-default (no argument)
>>
>> Thank you,
>>
>> Sabrina Yu
>>
>>
>>
>> ___
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>> 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
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>
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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 
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> but does not contain patient information, please contact the sender and 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] fast_selxavg3 error when Octave is used

2016-01-28 Thread Douglas Greve


Is that directory in your matlab path? does it run properly in matlab?

On 1/28/16 8:36 PM, m.abouelya...@gmail.com wrote:


Yes, it exists in the location you mentioned…


*From: *Douglas N Greve 
*Sent: *Friday, January 29, 2016 2:27 AM
*To: *freesurfer@nmr.mgh.harvard.edu 


*Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used

Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ?

On 01/28/2016 07:16 AM, m.abouelya...@gmail.com wrote:

>

> Since I am a windows user I got the Virtualbox version of FreeSurfer

> and to use fs fast, I installed Octave on the virtual machine, I set

> the environment variables and then when I run the command

>

> selxavg3-sess -analysis rtopy.lh -sf sessid

>

> which runs a retinotopy analysis, I get the following error:

>

> sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx

>

> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis

> rtopy.lh -sf sessid

>

> error: `fast_fileexists' undefined near line 5 column 4

>

> --

>

> ERROR: fast_selxavg3() failed\n

>

> Any idea of the cause of this error and how to run around?

>

> Thank you,

>

>

>

> ___

> Freesurfer mailing list

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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

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MGH-NMR Center

gr...@nmr.mgh.harvard.edu

Phone Number: 617-724-2358

Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] fast_selxavg3 error when Octave is used

2016-01-28 Thread Douglas Greve


yes

On 1/28/16 9:31 PM, m.abouelya...@gmail.com wrote:


I am running on the virtual machine where I don’t have MATLAB so I 
installed Octave…


Maybe I should include the folder into the Octave path?


*From: *Douglas Greve 
*Sent: *Friday, January 29, 2016 11:27 AM
*To: *m.abouelya...@gmail.com ; 
freesurfer@nmr.mgh.harvard.edu 

*Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used

Is that directory in your matlab path? does it run properly in matlab?

On 1/28/16 8:36 PM, m.abouelya...@gmail.com 
 wrote:


Yes, it exists in the location you mentioned…


*From: *Douglas N Greve 
*Sent: *Friday, January 29, 2016 2:27 AM
*To: *freesurfer@nmr.mgh.harvard.edu

*Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used

Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ?

On 01/28/2016 07:16 AM, m.abouelya...@gmail.com
 wrote:

>

> Since I am a windows user I got the Virtualbox version of
FreeSurfer

> and to use fs fast, I installed Octave on the virtual machine, I
set

> the environment variables and then when I run the command

>

> selxavg3-sess -analysis rtopy.lh -sf sessid

>

> which runs a retinotopy analysis, I get the following error:

>

> sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx

>

> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -analysis

> rtopy.lh -sf sessid

>

> error: `fast_fileexists' undefined near line 5 column 4

>

> --

>

> ERROR: fast_selxavg3() failed\n

>

> Any idea of the cause of this error and how to run around?

>

> Thank you,

>

>

>

> ___

> 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

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Re: [Freesurfer] Wm correction

Thanks, I also have another major problem with the subjects I am working on.Two 
of the subjects intend to freeze at #@# Fix Topology rh step while running 
reconstruction process.
 CORRECTING DEFECT 12 (vertices=29993, convex hull=7603)
I will upload one of the subjects to your ftp site, if you could take a look to 
see what is the defect.
Really appreciate your help in advance,
Maryam

Regards,Maryam Kouchakidivkolaei 

 On Thursday, January 28, 2016 5:51 PM, Bruce Fischl 
 wrote:

 Hi MaryamWe are working hard to get it out, but it's not quite ready yet. We 
will make an announcement when we have a beta versionBruce
On Jan 28, 2016, at 8:25 PM, maryam koochaki  wrote:

Hi Bruce,
How can I download version 6?

Best,Maryam

Regards,Maryam Kouchakidivkolaei 

On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
 wrote:

 Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> Ventricle. As you can see in the image attached, the big part is excluded in
> both hemisphere. I tried to fill it by editing wm volume but the problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05 {Disarmed}

what was the command line and screen output of the binarization? And are 
you saying that pre-binarization you have locations that are above 
threshold, but they are set to 0 anyway?


On Thu, 28 Jan 2016, Erik Lindberg wrote:


Dear Bruce and Freesufers,


I get the following message:


surfer: Interpreting overlay 
volume/media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glm
dir/Gend/thresholded.mgh as encoded scalar volume.


the two volumes I tried to convert: 

1)

Volume information for sig.mgh
  type: MGH
    dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
    xstart: -81921.0, xend: 81921.0
    ystart: -0.5, yend: 0.5
    zstart: -0.5, zend: 0.5
    TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   0., z_a =   1., c_a =
0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
0.

talairach xfm : 
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 81921.
    0.   0.   1.    -0.5000
    0.  -1.   0. 0.5000
    0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0. 81921.
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 0.5000
    0.   0.   0. 1.


2)


Volume information for cache.th13.abs.sig.cluster.mgh
  type: MGH
    dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
    xstart: -81921.0, xend: 81921.0
    ystart: -0.5, yend: 0.5
    zstart: -0.5, zend: 0.5
    TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   0., z_a =   1., c_a =
0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
0.

talairach xfm : 
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 81921.
    0.   0.   1.    -0.5000
    0.  -1.   0. 0.5000
    0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0. 81921.
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 0.5000
    0.   0.   0. 1.


Although both these overlays have significant areas - nothing appears on the
binarized version after the conversion


Best wishes,

Olof Lindberg

Olof Lindberg PhD
Novum plan 5
NVS department section clinical geriatrics
14186 Stockholm
+46722255711
MailScanner has detected a possible fraud attempt from "email.ki.se"
claiming to be http://www.oloflindberg.se

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Re: [Freesurfer] Wm correction

Hi Maryam
We are working hard to get it out, but it's not quite ready yet. We will make 
an announcement when we have a beta version
Bruce

> On Jan 28, 2016, at 8:25 PM, maryam koochaki  
> wrote:
> 
> Hi Bruce,
> How can I download version 6?
> 
> 
> Best,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> Regards,
> Maryam Kouchakidivkolaei
> 
> 
> On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
>  wrote:
> 
> 
> Hi Maryam
> 
> have you look at the aseg? I suspect that it didn't properly handle the 
> very large ventricles in this subject. Try manually editing it. V6 
> handles this kind of thing significantly better
> 
> cheers
> Bruce
> 
> On Thu, 28 Jan 2016, maryam 
> koochaki wrote:
> 
> > Hi Bruce,
> > I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> > Ventricle. As you can see in the image attached, the big part is excluded in
> > both hemisphere. I tried to fill it by editing wm volume but the problem
> > still exists.
> > Do you have any suggestion?
> > Thanks,
> > Maryam
> >  
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> >
> 
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[Freesurfer] Segmentation depends on image file format

2016-01-28 Thread Parzer, Peter

Hi,

we have brain images stored as DICOM and as NIFTI files. For some time we used 
to import the NIFTI files to freesurfer for segmentation. I was curious if it 
makes a difference if we would import the DICOM files directly, and was 
surprised that it actually did. Here are the commands we used:

# Import DICOM files
recon-all -s 3003PC_dcm -i 
../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm

# Convert DICOM to NIFTI and import NIFTI file
mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm 3003PC.nii.gz
recon-all -s 3003PC_nii -i 3003PC.nii.gz

# Segmentation of DICOM file import
recon-all -s 3003PC_dcm -all

# Segmentation of NIFTI file import
recon-all -s 3003PC_nii -all

Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import)

  1   4  5612 5611.8  Left-Lateral-Ventricle27.6355
12.8465 8.93.85. 
  2   5   452  452.2  Left-Inf-Lat-Vent 42.1100
14.9377 7.86.79. 
  3   7 1376513765.1  Left-Cerebellum-White-Matter  87.7808 
6.600836.   109.73. 

and here the the first 3 volumes for 3003PC_nii (NIFTI import)

  1   4  5582 5582.2  Left-Lateral-Ventricle27.4507
12.7212 8.93.85. 
  2   5   421  421.1  Left-Inf-Lat-Vent 40.8032
14.6554 7.83.76. 
  3   7 1389913898.6  Left-Cerebellum-White-Matter  87.6707 
6.753936.   109.73. 

The differences are small but I think there should be no differences at all. 
Has someone an explanation for this differences and which file format is better?

Greetings
Peter

P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on Ubuntu 
14.04 
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Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

Hi Will

it looks like there is incomplete myelination, which is probably part of 
your problem. You could try manually adjusting the transform in 
tkregister2

cheers
Bruce
On Thu, 28 Jan 2016, will brown wrote:

Hi Bruce,
I've attached a shot of the misalignment as seen in freeview.
Yes the original images were DICOM created in Siemens machine T1, 0.8 slice
thickness, can provide all DICOM tags if needed.

Thanks,
Will

On Tue, Jan 26, 2016 at 6:00 AM, 
wrote:
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     2. recon -all errors (Jasmin Alves)
     3. Re: Processing .mnc files (Ankita Chatterjee)
     4. Re: Processing .mnc files (Bruce Fischl)
     5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
        thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg)
     6. hippocampal subfields - multispectral segmentation       
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     7. Re: hippocampal subfields - multispectral segmentation   
  with
        FLAIR (Eugenio Iglesias)
     8. Re: recon -all errors (Bruce Fischl)
     9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
        thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl)
    10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
        thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg)
    11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
        thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl)
    12. FDR map: hide very little cluster (std...@virgilio.it)
    13. [All] position available immediately (Bruce Fischl)
    14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
        thresholded.mgh 1.3 = -log10(.05) (Douglas Greve)
    15. Re: FDR map: hide very little cluster (Douglas Greve)
    16. R: Re:  FDR map: hide very little cluster
  (std...@virgilio.it)
    17. R: Re:  FDR map: hide very little cluster
  (std...@virgilio.it)
    18. Re: R: Re: FDR map: hide very little cluster (Douglas N
  Greve)
    19. R:  R: Re:  FDR map: hide very little cluster
  (std...@virgilio.it)
    20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N
  Greve)
    21. R: Re:  R: Re: FDR map: hide very little cluster
        (std...@virgilio.it)

  --

  Message: 1
  Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST)
  From: Bruce Fischl 
  Subject: Re: [Freesurfer] mritotal failed - help with manual
          registration
  To: Freesurfer support list 
  Message-ID:

  Content-Type: text/plain; charset=US-ASCII; format=flowed

  Hi Will

  can you take the same images with freeview and send them along?
  Also:
  tell us a bit about your images. What format did they start in?
  Were they
  dicoms?

  Bruce

  On Mon, 25 Jan 2016, will brown wrote:

  > Hi all,
  > After attempting recon-all I received the error "mritotal
  failed, see
  > transforms/talairach.log" etc which I understand may have
  something to do
  > with bad output from registration. I've checked orig.mgz which
  does look out
  > of line - the orientation is off so that it appears the
  subject has their
  > head tilted off to one side (see Image1.jpg).
  >
  > I have tried to fix this manually with the help of this
  tutorial:
  >
  > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview
  >
  > Hovever, the "movable" blurry image that I'm trying to line up
  with my
  > subjects image does not match the coronal, sagittal or
  horizontal views,
  > e.g. when I click "coronal" my subject is displayed correctly
  but the
  > movable image is displayed horizontally (see Image2.jpg and
  Image3.jpg).
  >
  > Am I missing something obvious? (and am I even on the right
  track given this
  > error?)
  >
  > Thanks in advance for any help.
  >
  > Cheers,
  > Will
  >
  >

  --

  Message: 2
  Date: Sun, 24 Jan

Re: [Freesurfer] Wm correction


Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better


cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:



Hi Bruce,
I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
Ventricle. As you can see in the image attached, the big part is excluded in
both hemisphere. I tried to fill it by editing wm volume but the problem
still exists.
Do you have any suggestion?
Thanks,
Maryam
 








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Re: [Freesurfer] Fwd: hardware question