[Freesurfer] Freesurfer dev version: Hyppocampus, amygdala and thalamus segementation

[Steve Petersen]

External Email - Use Caution

 Dear Freesurfer devs,

We are considering segmenting with the Freesurfer 6 dev version the
hippocampus, the amygdala and the thalamus of several subjects who have
already done the recon-all. Since we have a T1 image and T2 image with
smaller voxel size, we have thought about using the *mode B: segmetation
with an additional scan* as explained in the freesurfer webpage. In
addition to voxel size, both images have slight differences in acquisition
parameters. Taking into account this situation we have these questions:

- Since there are other slightly different parameters between image T1 and
T2 in addition to voxel size (e.g. matrix size), it is correct to use B
mode with additional scan or we should use multispectral segmentation?

- Is it necessary to make some previous modification on some image before
running the script segment_HA.sh (e.g. coregister both images)?

- Is there a quality control that you can recommend after segmenting these
structures?


Thanks for your help!


Best regards,
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[Freesurfer] Freesurfer dev version not available on the server

[Scheffler, F, Mev [fre...@sun.ac.za]]

External Email - Use Caution

Dear Freesurfer Developers

I’ve been trying to download the development version but I keep getting an 
error message.

Error: The share does not exist on the server. Please check the share name, and 
then try again.

Any suggestions or alternatives?

Thanks very much for your help.

Kind regards,


FREDA SCHEFFLER

Researcher / PhD Candidate


[email.jpg]


MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika

Tel:  +27 21 938 9771
Email | E-pos:  fre...@sun.ac.za



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Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

[Douglas N. Greve]

How does the input image look, ie, orig.mgz?


On 04/19/2018 09:49 AM, Jones, Richard wrote:
>
> I ran the command shown below to do recon-all on DICOM images from a 
> Philips Ingenia scanner using the development version of freesurfer on 
> a Mac running high Sierra.
>
> recon-all -i 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm -subject 
> HOPE_SS020 –all
>
> The program crashed with the error “ERROR: mpr2mni305 failed, see 
> transforms/talairach_avi.log”
>
> The talairach_avi.log file is shown below, followed by the log file. 
> As a test I ran the same command, on the same data, using Freesurfer 6 
> and that ran without problems (except that it didn’t handle the 
> diffusion tags in the Philips DICOM header correctly so I had to set 
> FS_LOAD_DWI=0, this was not a problem in the development version). Any 
> suggestions as to what may be causing the problems with the library in 
> the development version?
>
> Thanks,
>
> Richard
>
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri
>
> /Applications/freesurfer_dev/bin/talairach_avi
>
> --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
>
> Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
> 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
>
> Thu Apr 19 08:45:01 EDT 2018
>
> mri_convert.bin orig_nu.mgz talsrcimg.img
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from orig_nu.mgz...
>
> TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
>
> i_ras = (-1, 7.45058e-09, 0)
>
> j_ras = (3.72529e-09, -4.88944e-09, -1)
>
> k_ras = (0, 1, 4.88944e-09)
>
> writing to talsrcimg.img...
>
> Analyze Output Matrix
>
> -1.0   0.0   0.0   128.15305;
>
> 0.0  -0.0   1.0  -116.15433;
>
> 0.0  -1.0   0.0   128.60870;
>
> 0.0   0.0   0.0   1.0;
>
> 
>
> INFO: set hdr.hist.orient to -1
>
> mpr2mni305 talsrcimg
>
> Thu Apr 19 08:45:02 EDT 2018
>
> /Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
>
> $Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
>
> target=711-2C_as_mni_average_305
>
> -
>
> analyzeto4dfp talsrcimg -O0 -y
>
> -
>
> $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
>
> Thu Apr 19 08:45:02 2018
>
> Writing: talsrcimg.4dfp.hdr
>
> $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
>
> Reading: talsrcimg.hdr
>
> header size 348 bytes
>
> hdr.dime.datatype offset=70    value=2
>
> hdr.dime.bitpix offset=72    value=8
>
> hdr.hist.orient offset=252  value=-1
>
> dimensionality 4
>
> dimensions   256   256 256 1
>
> Reading: talsrcimg.img
>
> Writing: talsrcimg.4dfp.img
>
> Writing: talsrcimg.4dfp.ifh
>
> ifh2hdr talsrcimg -r0to255
>
> ori=2
>
> -
>
> gauss_4dfp talsrcimg 1.1
>
> -
>
> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
>
>   Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
>
>   Reason: image not found
>
> Abort
>
> ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
>
> ERROR: mpr2mni305 execution aborted
>
> Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
>
> Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
>
> INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
>
> Actual FREESURFER_HOME /Applications/freesurfer_dev
>
> Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
> 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
>
> /Applications/freesurfer_dev/subjects/HOPE_SS020
>
> \n mri_convert 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
>
> mri_convert.bin 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
>
> Starting DICOMRead2()
>
> dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
>
> dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
>
> Ref Series No = 301
>
> Found 202 files, checking for dicoms
>
> Found 200 dicom files in series.
>
> First Sorting
>
> Computing Slice Direction
>
> Vs: -0.897217 -0.0611658 0.0354633
>
> Vs: -0.996909 -0.0679621 0.0394038
>
> Second Sorting
>
> IsDWI = 0, IsPhilipsDWI = 0
>
> Counting frames
>
> nframes = 1
>
> nslices = 200
>
> ndcmfiles = 200
>
> PE Dir = ROW (dicom read)
>
> Loading pixel data
>
> TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
>
> i_ras = (0.0644896, -0.994415, 0.0835493)
>
> j_ras = 

Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

[Hoopes, Andrew]

Hi Richard, thanks for pointing this out – I’ll take a look into it.

best
Andrew

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Jones, Richard" 
<richard.jo...@choa.org>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, April 19, 2018 at 9:49 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

I ran the command shown below to do recon-all on DICOM images from a Philips 
Ingenia scanner using the development version of freesurfer on a Mac running 
high Sierra.

recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
-subject HOPE_SS020 –all

The program crashed with the error “ERROR: mpr2mni305 failed, see 
transforms/talairach_avi.log”

The talairach_avi.log file is shown below, followed by the log file. As a test 
I ran the same command, on the same data, using Freesurfer 6 and that ran 
without problems (except that it didn’t handle the diffusion tags in the 
Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a 
problem in the development version). Any suggestions as to what may be causing 
the problems with the library in the development version?

Thanks,

Richard

/Applications/freesurfer_dev/subjects/HOPE_SS020/mri
/Applications/freesurfer_dev/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Thu Apr 19 08:45:01 EDT 2018
mri_convert.bin orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig_nu.mgz...
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (-1, 7.45058e-09, 0)
j_ras = (3.72529e-09, -4.88944e-09, -1)
k_ras = (0, 1, 4.88944e-09)
writing to talsrcimg.img...
Analyze Output Matrix
-1.0   0.0   0.0   128.15305;
0.0  -0.0   1.0  -116.15433;
0.0  -1.0   0.0   128.60870;
0.0   0.0   0.0   1.0;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Thu Apr 19 08:45:02 EDT 2018
/Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
target=711-2C_as_mni_average_305

-
analyzeto4dfp talsrcimg -O0 -y
-

$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Thu Apr 19 08:45:02 2018
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatype  offset=70value=2
hdr.dime.bitpix offset=72value=8
hdr.hist.orient   offset=252  value=-1
dimensionality 4
dimensions   256   256   256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2

-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
  Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
  Reason: image not found
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted


Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
Actual FREESURFER_HOME /Applications/freesurfer_dev
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Applications/freesurfer_dev/subjects/HOPE_SS020
\n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
Starting DICOMRead2()
dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
Ref Series No = 301
Found 202 files, checking for dicoms
Found 200 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.897217 -0.0611658 0.0354633
Vs: -0.996909 -0.0679621 0.0394038
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 200
ndcmfiles = 200
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (0.0644896, -0.994415, 0.0835493)
j_ras = (0.0

[Freesurfer] Freesurfer dev version : recon all error mpr2mni305

[Jones, Richard]

I ran the command shown below to do recon-all on DICOM images from a Philips 
Ingenia scanner using the development version of freesurfer on a Mac running 
high Sierra.

recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
-subject HOPE_SS020 -all

The program crashed with the error "ERROR: mpr2mni305 failed, see 
transforms/talairach_avi.log"

The talairach_avi.log file is shown below, followed by the log file. As a test 
I ran the same command, on the same data, using Freesurfer 6 and that ran 
without problems (except that it didn't handle the diffusion tags in the 
Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a 
problem in the development version). Any suggestions as to what may be causing 
the problems with the library in the development version?

Thanks,

Richard

/Applications/freesurfer_dev/subjects/HOPE_SS020/mri
/Applications/freesurfer_dev/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Thu Apr 19 08:45:01 EDT 2018
mri_convert.bin orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig_nu.mgz...
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (-1, 7.45058e-09, 0)
j_ras = (3.72529e-09, -4.88944e-09, -1)
k_ras = (0, 1, 4.88944e-09)
writing to talsrcimg.img...
Analyze Output Matrix
-1.0   0.0   0.0   128.15305;
0.0  -0.0   1.0  -116.15433;
0.0  -1.0   0.0   128.60870;
0.0   0.0   0.0   1.0;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Thu Apr 19 08:45:02 EDT 2018
/Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
target=711-2C_as_mni_average_305

-
analyzeto4dfp talsrcimg -O0 -y
-

$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Thu Apr 19 08:45:02 2018
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatype  offset=70value=2
hdr.dime.bitpix offset=72value=8
hdr.hist.orient   offset=252  value=-1
dimensionality 4
dimensions   256   256   256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2

-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
  Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
  Reason: image not found
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted


Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
Actual FREESURFER_HOME /Applications/freesurfer_dev
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Applications/freesurfer_dev/subjects/HOPE_SS020
\n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
Starting DICOMRead2()
dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
Ref Series No = 301
Found 202 files, checking for dicoms
Found 200 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.897217 -0.0611658 0.0354633
Vs: -0.996909 -0.0679621 0.0394038
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 200
ndcmfiles = 200
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (0.0644896, -0.994415, 0.0835493)
j_ras = (0.0448617, -0.08075, -0.995724)
k_ras = (0.996909, 0.0679621, 0.0394038)
writing to /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz...
#
#@# MotionCor Thu Apr 19 08:44:06 EDT 2018
Found 1 runs
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the 

Re: [Freesurfer] dev version

[Iglesias Gonzalez, Eugenio]

Dear Zheng,
Question 1: In the dev version, all labels are rendered by default. In previous 
versions: it’s probably best to open the file twice, and render the hippo with 
the range 200-249 and the amygdala with the range 7000-7020.
Question 2: open  lh.hippoAmygLabels-T1.v2x.mgz instead of  
lh.hippoAmygLabels-T1.v2x.FS60.mgz
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 郑凤莲 
<13181786...@163.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 1 February 2018 at 07:03
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] dev version

Hi all experts,
  I am using freesurfer dev version for segmentation of hippocampus and 
amydala. I have a doubt about it.
  1. In FS 6.0, I can type '203-226' in freeview for viewing subfields of 
hippocampus. In dev version, When I type 'freeview -v nu.mgz -v 
lh.hippoAmygLabels-T1.v2x.FS60.mgz:colormap=lut', there are subfields of 
hippocampus and amydala. How can I view them respectively, and get 
corresponding colors to every subfield?
  2. The hippoSFvolumes.txt shows the volume of body and head of some 
subfields, such as CA1, CA3. But  When I type 'freeview -v nu.mgz -v 
lh.hippoAmygLabels-T1.v2x.FS60.mgz:colormap=lut', it seems to serve the body 
and head as a whole. Is there any way to resolve it?

Sincerely,
Zheng





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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.

[Freesurfer] dev version

[郑凤莲]

Hi all experts,
  I am using freesurfer dev version for segmentation of hippocampus and 
amydala. I have a doubt about it.
  1. In FS 6.0, I can type '203-226' in freeview for viewing subfields of 
hippocampus. In dev version, When I type 'freeview -v nu.mgz -v 
lh.hippoAmygLabels-T1.v2x.FS60.mgz:colormap=lut', there are subfields of 
hippocampus and amydala. How can I view them respectively, and get 
corresponding colors to every subfield?
  2. The hippoSFvolumes.txt shows the volume of body and head of some 
subfields, such as CA1, CA3. But  When I type 'freeview -v nu.mgz -v 
lh.hippoAmygLabels-T1.v2x.FS60.mgz:colormap=lut', it seems to serve the body 
and head as a whole. Is there any way to resolve it?


Sincerely,
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Re: [Freesurfer] Freesurfer dev version

[Iglesias, Eugenio]

Hi Daniel,
The issue is fixed, but I don’t know if the updated version is already in dev.
Zeke, can you shed some light on this?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 1 Aug 2016, at 19:49, Liu, Daniel <d...@mcw.edu<mailto:d...@mcw.edu>> wrote:

It was the invalid MEX file problem mentioned in this exchange 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html

I was told it would be fixed sometime this week in the dev version (and in 2 
weeks when the next beta version was released).

Thanks,

Daniel

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bruce Fischl 
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
Sent: Monday, August 1, 2016 11:04 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer dev version

which error? The mri_normalize problem? If so, then yes I believe that is
now fixed
On Mon, 1 Aug 2016, Liu, Daniel wrote:

Hi,


I wanted to follow up on the error that came up in the freesurfer dev version 
this past week.  Has it been fixed yet?  If so, has the link to the download 
page been changed?  The one I booked marked does not lead me to the page 
anymore and I would appreciate it if you could direct me to the correct 
location.


Thanks,


Daniel

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Re: [Freesurfer] Freesurfer dev version

[Bruce Fischl]

which error? The mri_normalize problem? If so, then yes I believe that is 
now fixed
On Mon, 1 Aug 2016, Liu, Daniel wrote:

> Hi,
>
>
> I wanted to follow up on the error that came up in the freesurfer dev version 
> this past week.  Has it been fixed yet?  If so, has the link to the download 
> page been changed?  The one I booked marked does not lead me to the page 
> anymore and I would appreciate it if you could direct me to the correct 
> location.
>
>
> Thanks,
>
>
> Daniel
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] Freesurfer dev version

[Liu, Daniel]

Hi,


I wanted to follow up on the error that came up in the freesurfer dev version 
this past week.  Has it been fixed yet?  If so, has the link to the download 
page been changed?  The one I booked marked does not lead me to the page 
anymore and I would appreciate it if you could direct me to the correct 
location.


Thanks,


Daniel

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Re: [Freesurfer] dev version of mri_ca_label memory leak?

[Bruce Fischl]

you can probably just email them to me as they aren't terribly big. Make 
sure you get every file that is on the mri_ca_label command line


cheers
Bruce
On Thu, 30 
Jul 2015, Chris Adamson wrote:



Ok how can I send you the files and commands?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, 30 July 2015 12:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak?

Hi Chris

if you send me all the inputs to mri_ca_label and your exact command line I'll 
see if I can replicate it and either fix it or send you a new version. Or you 
can try the current dev version and see if it fixes things

cheers
Bruce
On Wed, 29 Jul 2015, Chris Adamson wrote:



Devs,

 

I’m running the CVS version of Freesurfer, checked out on 28/7/2015
(7/28/2015 for US people). I get to the –calabel step and mri_ca_label
takes a *long* time
(400 minutes) and uses a *lot* of memory. After it outputs “saving
sequentially combined intensity scales to
aseg.auto_noCCseg.label_intensities.txt” the memory consumption continues to 
increase. Currently it is at 8.9GB.

 

Can I send output to help debug this?

 

Chris.

 

Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research
Institute Murdoch Childrens Research Institute Royal Children’s
Hospital Flemington Road, Parkville, Victoria  3052, Australia
www.mcri.edu.au

E   chris.adam...@mcri.edu.au
T   03 9936 6780

 


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Re: [Freesurfer] dev version of mri_ca_label memory leak?

[Chris Adamson]

Ok I will send you the 001.mgz file, the build instructions file that I used 
and the commands that I used.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, 30 July 2015 11:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak?

you can probably just email them to me as they aren't terribly big. Make sure 
you get every file that is on the mri_ca_label command line

cheers
Bruce
On Thu, 30
Jul 2015, Chris Adamson wrote:

 Ok how can I send you the files and commands?

 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
 Fischl
 Sent: Thursday, 30 July 2015 12:03 AM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak?

 Hi Chris

 if you send me all the inputs to mri_ca_label and your exact command 
 line I'll see if I can replicate it and either fix it or send you a 
 new version. Or you can try the current dev version and see if it 
 fixes things

 cheers
 Bruce
 On Wed, 29 Jul 2015, Chris Adamson wrote:


 Devs,

  

 I’m running the CVS version of Freesurfer, checked out on 28/7/2015
 (7/28/2015 for US people). I get to the –calabel step and 
 mri_ca_label takes a *long* time
 (400 minutes) and uses a *lot* of memory. After it outputs “saving 
 sequentially combined intensity scales to 
 aseg.auto_noCCseg.label_intensities.txt” the memory consumption continues to 
 increase. Currently it is at 8.9GB.

  

 Can I send output to help debug this?

  

 Chris.

  

 Dr Chris Adamson
 Research Officer, Developmental Imaging, Murdoch Childrens Research 
 Institute Murdoch Childrens Research Institute Royal Children’s 
 Hospital Flemington Road, Parkville, Victoria  3052, Australia 
 www.mcri.edu.au

 E   chris.adam...@mcri.edu.au
 T   03 9936 6780

  


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Re: [Freesurfer] dev version of mri_ca_label memory leak?

[Chris Adamson]

Ok how can I send you the files and commands?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, 30 July 2015 12:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak?

Hi Chris

if you send me all the inputs to mri_ca_label and your exact command line I'll 
see if I can replicate it and either fix it or send you a new version. Or you 
can try the current dev version and see if it fixes things

cheers
Bruce
On Wed, 29 Jul 2015, Chris Adamson wrote:

 
 Devs,
 
  
 
 I’m running the CVS version of Freesurfer, checked out on 28/7/2015 
 (7/28/2015 for US people). I get to the –calabel step and mri_ca_label 
 takes a *long* time
 (400 minutes) and uses a *lot* of memory. After it outputs “saving 
 sequentially combined intensity scales to 
 aseg.auto_noCCseg.label_intensities.txt” the memory consumption continues to 
 increase. Currently it is at 8.9GB.
 
  
 
 Can I send output to help debug this?
 
  
 
 Chris.
 
  
 
 Dr Chris Adamson
 Research Officer, Developmental Imaging, Murdoch Childrens Research 
 Institute Murdoch Childrens Research Institute Royal Children’s 
 Hospital Flemington Road, Parkville, Victoria  3052, Australia 
 www.mcri.edu.au
 
 E   chris.adam...@mcri.edu.au
 T   03 9936 6780
 
  
 
 
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Re: [Freesurfer] dev version of mri_ca_label memory leak?

[Bruce Fischl]

Hi Chris

if you send me all the inputs to mri_ca_label and your exact command line 
I'll see if I can replicate it and either fix it or send you a new 
version. Or you can try the current dev version and see if it fixes 
things


cheers
Bruce
On Wed, 29 Jul 2015, Chris Adamson wrote:



Devs,

 

I’m running the CVS version of Freesurfer, checked out on 28/7/2015 (7/28/2015
for US people). I get to the –calabel step and mri_ca_label takes a *long* time
(400 minutes) and uses a *lot* of memory. After it outputs “saving sequentially
combined intensity scales to aseg.auto_noCCseg.label_intensities.txt” the memory
consumption continues to increase. Currently it is at 8.9GB.

 

Can I send output to help debug this?

 

Chris.

 

Dr Chris Adamson  
Research Officer, Developmental Imaging, Murdoch Childrens Research Institute 
Murdoch Childrens Research Institute 
Royal Children’s Hospital
Flemington Road, Parkville, Victoria  3052, Australia
www.mcri.edu.au

E   chris.adam...@mcri.edu.au
T   03 9936 6780  

 


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[Freesurfer] dev version of mri_ca_label memory leak?

[Chris Adamson]

Devs,

I'm running the CVS version of Freesurfer, checked out on 28/7/2015 (7/28/2015 
for US people). I get to the -calabel step and mri_ca_label takes a *long* time 
(400 minutes) and uses a *lot* of memory. After it outputs saving sequentially 
combined intensity scales to aseg.auto_noCCseg.label_intensities.txt the 
memory consumption continues to increase. Currently it is at 8.9GB.

Can I send output to help debug this?

Chris.

Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research Institute
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road, Parkville, Victoria  3052, Australia
www.mcri.edu.auhttp://www.mcri.edu.au/
E   chris.adam...@mcri.edu.au
T   03 9936 6780


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[Freesurfer] Dev Version

[Hassan bakhshi]

Hi
I downloaded the centos 6 freeview.bin and replaced it into
$freesurferhome/bin/freeview.bin

but now i cant open freeview, it says that it is not a executable file and
it is binary.

i wanted to test hippocampal subfields.

Kind regards
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Re: [Freesurfer] Dev Version

[dgw]

Did you check the permissions? You have to make sure the permissions are 
executable.

HTH
D

On 5/26/15 6:33 AM, Hassan bakhshi wrote:
 Hi
 I downloaded the centos 6 freeview.bin and replaced it into
 $freesurferhome/bin/freeview.bin

 but now i cant open freeview, it says that it is not a executable file and
 it is binary.

 i wanted to test hippocampal subfields.

 Kind regards



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Re: [Freesurfer] Dev Version

[Bruce Fischl]

Hi Hassan

try:

chmod a+x FREESURFER_HOME/bin/freeview.bin

cheers
Bruce

On Tue, 26 May 2015, Hassan 
bakhshi wrote:



Hi I downloaded the centos 6 freeview.bin and replaced it into
$freesurferhome/bin/freeview.bin

but now i cant open freeview, it says that it is not a executable file and
it is binary.

i wanted to test hippocampal subfields.

Kind regards

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[Freesurfer] dev version of mri_glmfit for intel macs

[Catherine Hartley]

Hi,

I'm getting a bus error when I run mri_glmfit on my Intel Mac.  When  
I had this problem before, I got a development version of mri_glmfit  
which solved the problem.  Unfortunately I've reinstalled a newer  
version of Freesurfer since then and overwrote that binary file and  
it's no longer on  the public distribution server.


If someone could repost the latest version of mri_glmfit for Intel  
Macs (10.4.9), that would be great.


The same problem is described here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04632.html

Thanks,
Cate
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Re: [Freesurfer] dev version of mri_glmfit for intel macs

[Nick Schmansky]

Cate,

There is a current dev distribution of freesurfer for the Intel Mac
here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/macintel

Its the .dmg file, which you can drag and drop to your desktop, then
double-click to start the install GUI.

A new mri_glmfit is also in that dir if you just want that.

Nick


On Mon, 2007-08-06 at 17:56 -0400, Catherine Hartley wrote:
 Hi,
 
 I'm getting a bus error when I run mri_glmfit on my Intel Mac.  When  
 I had this problem before, I got a development version of mri_glmfit  
 which solved the problem.  Unfortunately I've reinstalled a newer  
 version of Freesurfer since then and overwrote that binary file and  
 it's no longer on  the public distribution server.
 
 If someone could repost the latest version of mri_glmfit for Intel  
 Macs (10.4.9), that would be great.
 
 The same problem is described here:
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04632.html
 
 Thanks,
 Cate
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[Freesurfer] dev-version/new version question.

[Martin Ystad]

Hi, I'm currently using the freesurfer-Linux-centos4-dev20060210-full 
release, and I'm thinking of upgrading to the new stable release.
However, I've done a lot of processing with the 20060210-release, and 
I'm not very keen on starting all over again with the new release.
Do you recommend that I reprocess my subjects on the new stable release 
before doing a group study, or are they similar enough in terms of 
results, so that I don't need to?
In case I do need to run everything over, which steps do I need to rerun 
(certainly not all?), and can I keep my manual edits to the brainmask- 
or wm-volume?


Thanks,
Martin Ystad
University of Bergen, Norway.

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Re: [Freesurfer] dev-version/new version question.

[Jenni Pacheco]

As a note for everyone since this question has come up a lot, one of the 
many cool new features of recon-all is that it saves all of your edits, 
every time, by default.  You have to specify with certain flags when you 
want it to ignore your edits (see 
https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags for a list of 
flags).  This applies to edits to manual talairach registrations, seed 
points for cutting planes, control points for normalization, edits to the 
brainmask.mgz volume, edits to the wm.mgz volume, and edits to the 
aseg.mgz subcortical segmentation.  Every time you re-run anything that 
you have changed in these will be saved and used in subsequent steps. 
This should make re-running your subjects with a new version relatively 
painless.


Martin, in terms of your compatibility question, my recommendation is to 
always use the exact same version for a group study, its the only way you 
can be sure everything has been done consistently.  During the time 
between Feb 10 (your current version) and the release there were many 
changes made to the code, although off the top of my head I can't make any 
guesses as to how this may affect your group study.



Jenni

On Thu, 9 Mar 2006, Martin Ystad wrote:

Hi, I'm currently using the freesurfer-Linux-centos4-dev20060210-full 
release, and I'm thinking of upgrading to the new stable release.
However, I've done a lot of processing with the 20060210-release, and I'm not 
very keen on starting all over again with the new release.
Do you recommend that I reprocess my subjects on the new stable release 
before doing a group study, or are they similar enough in terms of results, 
so that I don't need to?
In case I do need to run everything over, which steps do I need to rerun 
(certainly not all?), and can I keep my manual edits to the brainmask- or 
wm-volume?


Thanks,
Martin Ystad
University of Bergen, Norway.

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