Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps
Hi Douglas, Thanks for the help! However, when I tried the --nofixmni flag, all the ROIs appeared to have identical MNI coordinates. I have pasted the output from 3 ROIS in the LH. # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZNVtxs 13.332 83949 82219.39-29.4 -22.0 17.4 163842 13.533 117158 82219.39-29.4 -22.0 17.4 163842 13.170 83424 82219.39-29.4 -22.0 17.4 163842 The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0). Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cannot find qdec file
Hi Doug,
this is the result it printed out in the terminal:
etsch:/scr/etsch2/kids$ mris_preproc --debug --qdec-long long.qdec.table.dat
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --qdec-long
shift
switch ( $flag )
switch ( --qdec-long )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = long.qdec.table.dat
shift
if ( ! -e $fsgdf ) then
if ( ! -e long.qdec.table.dat ) then
set sl = `cat $fsgdf | awk '{if ($1 != fsid substr($1,0,1) != #)
printf(%s.long.%s\n, $1, $2)}'` ;
set sl = `cat $fsgdf | awk '{if ($1 != fsid substr($1,0,1) != #)
printf(%s.long.%s\n, $1, $2)}'`
awk {if ($1 != fsid substr($1,0,1) != #) printf(%s.long.%s\n, $1, $2)}
cat long.qdec.table.dat
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( AL3K_1.long.AL3K.base AL3K_2.long.AL3K.base
AL3K_3.long.AL3K.base AM1K_1.long.AM1K.base AM1K_2.long.AM1K.base
AM1K_3.long.AM1K.base BJ4K_1.long.BJ4K.base BJ4K_2.long.BJ4K.base
BJ4K_3.long.BJ4K.base BJ8K_1.long.BJ8K.base BJ8K_2.long.BJ8K.base
BJ8K_3.long.BJ8K.base BN2K_1.long.BN2K.base BN2K_2.long.BN2K.base
BN2K_3.long.BN2K.base WL3K_1.long.WL3K.base WL3K_2.long.WL3K.base
WL3K_3.long.WL3K.base ZF1K_1.long.ZF1K.base ZF1K_2.long.ZF1K.base
ZF1K_3.long.ZF1K.base .long. )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto handle_fsfast ;
goto handle_fsfast
if ( $#SessFile ) then
if ( 0 ) then
goto handle_fsfast_return ;
goto handle_fsfast_return
goto check_params ;
goto check_params
if ( $#subjlistfile $#ivplist ) then
if ( 0 0 ) then
if ( $#subjlistfile $#fsgdf ) then
if ( 0 1 ) then
if ( $#ivplist $#fsgdf ) then
if ( 0 1 ) then
if ( $#subjlist == 0 ) then
if ( 22 == 0 ) then
if ( $#srchemi == 0 ) then
if ( 0 == 0 ) then
echo ERROR: no source hemi specified
echo ERROR: no source hemi specified
ERROR: no source hemi specified
exit 1 ;
exit 1
Cheers, Clara
- Ursprüngliche Mail -
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 13. August 2015 22:10:26
Betreff: Re: [Freesurfer] cannot find qdec file
I'm not sure what to tell you. When I use the new file I don't get an
error. When I use the old one I do. Can you run
mris_preproc --debug --qdec-long long.qdec.table.dat
and send me the result?
On 08/13/2015 01:01 PM, Clara Kühn wrote:
do you mean the one without the blank line at the end? I've attached that for
you.
Cheers, Clara
- Ursprüngliche Mail -
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 13. August 2015 18:12:40
Betreff: Re: [Freesurfer] cannot find qdec file
Can you send the new qdec table file?
On 08/05/2015 04:05 AM, Clara Kühn wrote:
no worries!
sadly, though, deleting the empty line wasn't the answer to the problem :(
Cheers, Clara
- Ursprüngliche Mail -
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 4. August 2015 20:43:47
Betreff: Re: [Freesurfer] cannot find qdec file
oops, sorry for the delay, thanks for the reminder. The problem is that
you have a blank line at the end of your long.qdec.table.dat file.
Remove the line and see if it works.
doug
On 08/04/2015 12:42 PM, Clara Kühn wrote:
Hi Doug,
did the fordoug.log file give any information about why FreeSurfer can't
find my qdec file?
Cheers and thanks for working on this!
Clara
- Ursprüngliche Mail -
Von: Douglas Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 3. August 2015 17:16:18
Betreff: Re: [Freesurfer] cannot find qdec file
can you run
mris_preproc --debug --qdec-long
/scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1
--hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh
| tee fordoug.log
and send me fordoug.log ?
On 8/3/15 10:38 AM, Clara Kühn wrote:
the command line is this:
mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat
--target 7kids_template_sc1 --hemi lh --meas thickness --out
/scr/etsch2/kids/ct/qdec/lh.thickness.mgh
the terminal output is this:
nsubjects = 22
ERROR: cannot find /scr/etsch2/kids/ct/.long.
and the actual qdec file is attached.
Cheers, Clara
- Ursprüngliche Mail -
Von: Douglas Greve gr...@nmr.mgh.harvard.edu An:
freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24
Betreff: Re: [Freesurfer] cannot find qdec file
Can you send your command line, full terminal output, and your
long.qdec.table.dat file?
On 8/3/15 10:31 AM, Clara Kühn wrote:
ok, it can only access the file if I type
ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash)
but if I then use that path for the mris_preproc command I get
nsubjects = 22
ERROR:
[Freesurfer] Is the fsaverage in the MNI space?
Dear freesurfer experts, The freesurfer online manual stated that before group analysis, we should resample data onto the common space (fsaverage). I have three questions here. First, Is the fsaverage file in the MNI space? In some previous studies, they report significant clusters with MNI coordinates. So, I would like to know whether this common space is equal to MNI space. Second, what does resample mean? Normalization--register the surf data to the fsaverage space? In my experience, I just used resample to change the voxel size in the volume data (e.g., before 1*1*1, after 3*3*3). The final question is that the fsaverage file is generated from my data or just a prior template? Thanks in advance. Best, Feng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Label or Overlay of Surface files
Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inflated), but surface overlays somehow don't load properly into 3D slicer, I am trying right surface files (lh.sulc , lh.curve e.g.)? On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhshmand saeedbakhshm...@gmail.com wrote: Hi Lee, Perfect, Thanks. Saeed On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu wrote: Hi Saeed, You can run either of the following commands to overlay the ?h.sulc or ?h.curv file: tksurfer subject hemisphere surface -snap file name -sulc tksurfer subject hemisphere surface -snap file name -curv Best, Lee On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: I used it as this:tksurfer subject hemisphere surface -snap file name -overlay file name And it adds a gray scale version of sulcus map to the plain gray, How can I activate colors? Thanks, Saeed On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: load them as curvature files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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 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 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] registering 2 scans
Hi Bruce, My goal is to compare the surfaces and segmentations from the reconstructions of the images from the 2 head coils. I'd like to be able to visualize the surfaces from both scans/coils on the same structural image. Thanks, Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, August 14, 2015 12:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] registering 2 scans Hi Matt can you tell us what your goal is for this analysis? You could use the longitudinal tools depending on what you are up to cheers Bruce On Fri, 14 Aug 2015, Hibert, Matthew Louis wrote: Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the memprage's from each coil with freesurfer. I'd now like to register these two reconstructions to each other, both the volumes and the surfaces. I've generated an lta registration matrix using mri_robust_register but am unsure how to apply this to other files. Is there a way to apply a registration matrix to all volume and surface files from a freesurfer reconstruction? Is there a better way to accomplish this? Thanks, Matt ___ 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] registering 2 scans
Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the memprage's from each coil with freesurfer. I'd now like to register these two reconstructions to each other, both the volumes and the surfaces. I've generated an lta registration matrix using mri_robust_register but am unsure how to apply this to other files. Is there a way to apply a registration matrix to all volume and surface files from a freesurfer reconstruction? Is there a better way to accomplish this? Thanks, Matt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] registering 2 scans
Hi Matt can you tell us what your goal is for this analysis? You could use the longitudinal tools depending on what you are up to cheers Bruce On Fri, 14 Aug 2015, Hibert, Matthew Louis wrote: Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the memprage's from each coil with freesurfer. I'd now like to register these two reconstructions to each other, both the volumes and the surfaces. I've generated an lta registration matrix using mri_robust_register but am unsure how to apply this to other files. Is there a way to apply a registration matrix to all volume and surface files from a freesurfer reconstruction? Is there a better way to accomplish this? Thanks, Matt ___ 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] Trakula
Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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] mris_make_surfaces error
Dear Freesurfer experts, I'm trying to run *mris_make_surfaces* with a FLAIR.mgz file as input. I used the same command as used if I run autorecon3, in order to make a pial refinement. Here is the command: mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR subject_name rh However, when I try to run this command individually I always get this error: ... smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning cortical surface to gray/csf boundary. repositioning pial surface locations using ../mri/FLAIR.mgz *mghRead(../mri/FLAIR.mgz, -1): could not open file* *mris_make_surfaces: could not load flair volume ../mri/FLAIR.mgz* The problem is that the output of mghRead is type NULL, and then the program exits with this error, as it can be seen in mri_make_surfaces.c: [image: Imágenes integradas 3] I have set up the same enviroment (SUBJECTS_DIR, etc) as if I run with autorecon3, so I can't understand why is this error happening. The FLAIR file mgz is not corrupted as I checked with tkmedit and mri_info. Could you give me some idea? Thanks in advance, Best, Marc ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Surface Loading Error
You have the most recent (i.e. development) version of freeview installed on top of the version 5.3 release of freesurfer. However, the development version of freeview has diverged to far from its original package, and is no longer compatible with freesurfer version 5.3. If you want to use the development version of freeview, you will need to install the development version of freesurfer, which can be downloaded from this page: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz If you wish to keep the version of freesurfer you already have you may simply install the dev version into an alternate location. For example, $ sudo mkdir /usr/local/freesurfer_dev $ tar -C /usr/local/freesurfer_dev -xzvf freesurfer-Darwin-lion-dev.tar.gz -Zeke On 08/11/2015 08:36 PM, Serdar AKKOL wrote: Dear Zeke Kaufman, I'm sending you this e-mail from Staford University, Laboratory Behavioral and Cognitive Neurology. We are new in using Freesurfer and had a problem in Surface Loading. I attached the error message we are getting. We are using the same version (v 1.379.2.73) on a similar computer without a problem. We hope that you would help us about this problem. We are ready to serve any other information you need. Thank you very much. Sincerely, Serdar Akkol Istanbul University Cerrahpasa Medical Faculty 4. grade $ freeview -f ./surf/lh.inflated -start_in_debugger Option 'start_in_debugger' not recognized.dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /usr/local/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /usr/local/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 5 TRAP [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a darwin12. named Franks-iMac.local by franksguest Tue Aug 11 16:25:34 2015 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_make_surfaces error
Hi Marc, You can try running this command, to complete all the steps in recon-all that use FLAIR images to improve your pial surfaces: recon-all -FLAIRpial -s subject_name Best, Lee On Fri, 14 Aug 2015, Marc Garriga Peguero wrote: Dear Freesurfer experts, I'm trying to run mris_make_surfaces with a FLAIR.mgz file as input. I used the same command as used if I run autorecon3, in order to make a pial refinement. Here is the command: mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR subject_name rh However, when I try to run this command individually I always get this error: ... smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning cortical surface to gray/csf boundary. repositioning pial surface locations using ../mri/FLAIR.mgz mghRead(../mri/FLAIR.mgz, -1): could not open file mris_make_surfaces: could not load flair volume ../mri/FLAIR.mgz The problem is that the output of mghRead is type NULL, and then the program exits with this error, as it can be seen in mri_make_surfaces.c: Imágenes integradas 3 I have set up the same enviroment (SUBJECTS_DIR, etc) as if I run with autorecon3, so I can't understand why is this error happening. The FLAIR file mgz is not corrupted as I checked with tkmedit and mri_info. Could you give me some idea? Thanks in advance, Best, Marc ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Label or Overlay of Surface files
SOLVED. On Fri, Aug 14, 2015 at 4:08 PM, Saeed Mahdizadeh Bakhshmand saeedbakhshm...@gmail.com wrote: Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inflated), but surface overlays somehow don't load properly into 3D slicer, I am trying right surface files (lh.sulc , lh.curve e.g.)? On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhshmand saeedbakhshm...@gmail.com wrote: Hi Lee, Perfect, Thanks. Saeed On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu wrote: Hi Saeed, You can run either of the following commands to overlay the ?h.sulc or ?h.curv file: tksurfer subject hemisphere surface -snap file name -sulc tksurfer subject hemisphere surface -snap file name -curv Best, Lee On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: I used it as this:tksurfer subject hemisphere surface -snap file name -overlay file name And it adds a gray scale version of sulcus map to the plain gray, How can I activate colors? Thanks, Saeed On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: load them as curvature files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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 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 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Label or Overlay of Surface files
Hi Saeed lh.sulc and lh.curv are scalar overlays, not surfaces. The surfaces are e.g. lh.inflated, lh.white, lh.pial, etc cheers Bruce On Fri, 14 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inflated), but surface overlays somehow don't load properly into 3D slicer, I am trying right surface files (lh.sulc , lh.curve e.g.)? On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhshmand saeedbakhshm...@gmail.com wrote: Hi Lee, Perfect, Thanks. Saeed On Thu, Aug 6, 2015 at 5:15 PM, Lee Tirrell ltirr...@nmr.mgh.harvard.edu wrote: Hi Saeed, You can run either of the following commands to overlay the ?h.sulc or ?h.curv file: tksurfer subject hemisphere surface -snap file name -sulc tksurfer subject hemisphere surface -snap file name -curv Best, Lee On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: I used it as this:tksurfer subject hemisphere surface -snap file name -overlay file name And it adds a gray scale version of sulcus map to the plain gray, How can I activate colors? Thanks, Saeed On Thu, Aug 6, 2015 at 4:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: load them as curvature files cheers Bruce On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: And are they treated as label files (e.g. lh.aparc.annot ) in the label directory? And how they can be added to the tksurfer snapshot procedure? On Thu, Aug 6, 2015 at 4:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, the scalar overlays are stored separately (e.g. lh.curv, lh.sulc, etc...) On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed ___ 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 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 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
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says export XAPPLRESDIR;, please insert this line of code: JAVA_TOOL_OPTIONS If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do some more research Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 10, 2015 9:01:26 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi Eugenio, I have about 128 GB of RAM memory in both machine. I got segmentation fault error in the new machine and not in the older one. I ran the test data (bert) and I get segmentation fault error. I think the only difference between the two machine is Ubuntu version. The new machine uses Ubuntu 15.04 while the older one uses 14.04. Both the machine has the same hardware configuration. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Sunday, August 9, 2015 6:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? 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 - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
Sorry, I actually meant: unset JAVA_TOOL_OPTIONS Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Eugenio Iglesias e.igles...@bcbl.eu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 14, 2015 11:51:54 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says export XAPPLRESDIR;, please insert this line of code: JAVA_TOOL_OPTIONS If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do some more research Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 10, 2015 9:01:26 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi Eugenio, I have about 128 GB of RAM memory in both machine. I got segmentation fault error in the new machine and not in the older one. I ran the test data (bert) and I get segmentation fault error. I think the only difference between the two machine is Ubuntu version. The new machine uses Ubuntu 15.04 while the older one uses 14.04. Both the machine has the same hardware configuration. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Sunday, August 9, 2015 6:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? 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 - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag
Hi Eugenio, Thank you for your help. I saw your first email and tried running with JAVA_TOOL_OPTIONS and it worked. It is still running without segmentation fault. After I finish that one I will run with unset JAVA_TOOL_OPTIONS. I will let you know the result of second run. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Friday, August 14, 2015 11:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Sorry, I actually meant: unset JAVA_TOOL_OPTIONS Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Eugenio Iglesias e.igles...@bcbl.eu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 14, 2015 11:51:54 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says export XAPPLRESDIR;, please insert this line of code: JAVA_TOOL_OPTIONS If it doesn't work, I'll install Ubuntu 15 on my laptop this weekiend and do some more research Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 10, 2015 9:01:26 AM Subject: Re: [Freesurfer] segmentation faultwhile running -hippocampal-subfields-T1 flag Hi Eugenio, I have about 128 GB of RAM memory in both machine. I got segmentation fault error in the new machine and not in the older one. I ran the test data (bert) and I get segmentation fault error. I think the only difference between the two machine is Ubuntu version. The new machine uses Ubuntu 15.04 while the older one uses 14.04. Both the machine has the same hardware configuration. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.igles...@bcbl.eu Sent: Sunday, August 9, 2015 6:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Prabesh, do you get the same error if you try rerunning the module on the same volume? Also, how much RAM memory does the machine have? 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 - Original Message - From: Prabesh Kanel pk...@my.fsu.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 7, 2015 9:06:51 PM Subject: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag Hi Freesurfer group, I am using freesurfer (Linux-centos6_x86_64 August 3rd) for segmenting subfield of hippocampus. I followed the instruction written and was able to segment hippocampus subfields for number of MR images in one of the server. I followed the same instruction in another server with same configurations but I am receiving segmentation error. The segmentation error comes due to matlab memory management. I have included the matlab crash dump file along with the message. Has anyone experience this problem?? Regards, Prabesh ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Registering surface files from fsaverage_sym to individual subjects
Dear FS experts Thanks for your help. Just to let you know I had registered rh .mgh files to the lh of fsaverage_sym in order to calculate inter hemispheric differences (lh minus rh). So, in order to transform back, I need to firstly register the .mgh file back to the right hemisphere and then register back to the individuals native space. This is what worked: mris_apply_reg --src $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh --trg $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh \ --streg $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg $SUBJECTS_DIR/fsaverage_sym/surf/rh.sphere.left_right mri_surf2surf --srcsubject fsaverage_sym --srcsurfval $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh --trgsubject $s --trgsurfval $s/surf/rh.lh-rh.w-g.pct.mgh --hemi rh --srcsurfreg sphere.reg --trgsurfreg sphere.reg Thanks, Sophie ___ 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.
